Device for analyzing a fluid sample

ABSTRACT

The present invention provides a cartridge for analyzing a fluid sample. The cartridge provides for the efficient separation of cells or viruses in the sample from the remaining sample fluid, lysis of the cells or viruses to release the analyte (e.g., nucleic acid) therefrom, and optionally chemical reaction and/or detection of the analyte. The cartridge is useful in a variety of diagnostic, life science research, environmental, or forensic applications for determining the presence or absence of one or more analytes in a sample.

RELATED APPLICATION INFORMATION

[0001] This application is a divisional of U.S. application Ser. No.09/583,807 filed May 30, 2000 which application is a continuation inpart of U.S. application Ser. No. 09/331,911 filed Jun. 25, 1999. Thisapplication and U.S. application Ser. No. 09/583,807 claim priority fromprovisional application Ser. No. 60/136,703 filed May 28, 1999. All ofthe above-referenced applications are incorporated by reference hereinfor all purposes.

FIELD OF THE INVENTION

[0002] The present invention relates generally to the field ofbiochemical analysis, and in particular to a cartridge for analyzing afluid sample.

BACKGROUND OF THE INVENTION

[0003] The analysis of clinical or environmental fluid samples generallyinvolves a series of chemical, optical, electrical, mechanical, orthermal processing steps on the samples. In recent years, there has beengrowing interest in developing disposable cartridges for conductinganalyses of biological samples for various diagnostic and monitoringpurposes. For example, U.S. Patent 5,587,128 to Wilding disclosesdevices for amplifying a preselected polynucleotide in a sample byconducting a polynucleotide amplification reaction. U.S. Pat. No.5,922,591 to Anderson et al. describes a miniaturized, integratednucleic acid diagnostic device and system. The device is generallycapable of performing one or more sample acquisition and preparationoperations, in combination with one or more sample analysis operations.

[0004] Prior fluidic cartridges for processing fluid samples havefocused on picoliter, nanoliter, and microliter sample volumes. Thesesmall sample volumes are not practical for many realistic diagnosticapplications. Of special interest is the detection of target analytes(e.g., nucleic acid) that exist in low concentrations in many samples.For example, in detecting infectious diseases, gram negative bacteriacan be present at less than 10 copies per milliliter of blood,cryptosporidium generally appears as only a few copies per gallon ofdrinking water, concentrated biothreat agents (e.g., anthrax) at lessthan 100 copies per milliliter of water, and food poisoning agents, suchas E. coli and salmonella, may be manifested in less than 10 copies pergram of food.

SUMMARY

[0005] The present invention provides a device for analyzing a fluidsample to determine the presence or absence of an analyte in the sample.The device comprises a cartridge for separating a desired analyte fromthe sample and for holding the analyte for chemical reaction and opticaldetection. The present invention also provides an instrument thatreceives the cartridge for sample processing. The desired analyte istypically intracellular material (e.g., nucleic acid, proteins,carbohydrates, lipids, bacteria, or intracellular parasites). In apreferred use, the analyte is nucleic acid which the cartridge separatesfrom the fluid sample and holds for amplification (e.g., using PCR) andoptical detection.

[0006] In a preferred embodiment, the cartridge is used with atransducer to separate an analyte from a fluid sample. The cartridge hasa sample port for introducing a sample into the cartridge, and a sampleflow path extending from the sample port. The cartridge also has alysing chamber in the sample flow path. The lysing chamber contains atleast one filter for capturing cells or viruses from the sample as thesample flows through the lysing chamber. The lysing chamber is definedby at least one wall having an external surface for contacting thetransducer to sonicate the lysing chamber. Beads may optionally bedisposed in the lysing chamber for rupturing the cells or viruses as thechamber is sonicated. The cartridge also includes a waste chamber influid communication with the lysing chamber via the sample flow path forreceiving the remaining sample fluid after the sample flows through thelysing chamber. The cartridge further includes a third chamber connectedto the lysing chamber via an analyte flow path for receiving the analyteseparated from the sample. The third chamber is preferably a reactionchamber for chemically reacting and optically detecting the analyte. Thecartridge also includes at least one flow controller (e.g., valves) fordirecting the sample into the waste chamber after the sample flowsthrough the lysing chamber and for directing the analyte separated fromthe sample into the third chamber. The design of the cartridge permitsthe efficient processing of large sample volumes to enable the accuratedetection of low concentration analytes.

BRIEF DESCRIPTION OF THE DRAWINGS

[0007]FIG. 1 is an isometric view of a cartridge for analyzing a fluidsample according to a first embodiment of the invention.

[0008]FIG. 2 is a lower isometric view of the cartridge of FIG. 1.

[0009]FIG. 3 is an exploded view of the cartridge of FIG. 1.

[0010]FIG. 4 is another exploded view of the cartridge of FIG. 1.

[0011]FIG. 5 is a partially cut away view of an ultrasonic horn coupledto a wall of a lysing chamber formed in the cartridge of FIG. 1.

[0012]FIG. 6 is an exploded view of a filter stack positioned in thelysing chamber of the cartridge of FIG. 1.

[0013]FIG. 7 is a top plan view of the cartridge of FIG. 1.

[0014]FIG. 8 is a bottom plan view of the cartridge of FIG. 1.

[0015]FIG. 9 is a schematic block diagram of the cartridge of FIG. 1.

[0016]FIG. 10 is an isometric view of an instrument into which thecartridge of FIG. 1 is placed for processing.

[0017]FIG. 11 is an isometric view of the cartridge of FIG. 1 in theinstrument of FIG. 10.

[0018]FIG. 12 is a partially cut-away view of the cartridge of FIG. 1 inthe instrument of FIG. 10.

[0019]FIG. 13 is a schematic, plan view of optical sensors positioned todetect liquid levels in the cartridge of FIG. 1.

[0020]FIG. 14 is a partially cut away, schematic, side view of a slottedoptical sensor positioned to detect the liquid level in a sensor chamberof the cartridge of FIG. 1.

[0021]FIG. 15A is a cross-sectional view of a portion of the body of thecartridge of FIG. 1 illustrating two different types of valves in thecartridge.

[0022]FIG. 15B is a cross-sectional view of the valves of FIG. 15A in aclosed position.

[0023]FIG. 16A is another cross-sectional view of one of the valves ofFIG. 15A in an open position.

[0024]FIG. 16B is a cross-sectional view of the valve of FIG. 16A in aclosed position.

[0025] FIGS. 17-19 illustrate a valve actuation system for opening andclosing the valves of FIG. 15A.

[0026]FIG. 20 is a cross sectional view of alternative valve actuatorsfor opening and closing the valves in the cartridge of FIG. 1. FIG. 20also shows a pressure delivery nozzle sealed to a pressure port formedin the cartridge of FIG. 1.

[0027]FIG. 21 is a partially exploded, isometric view of a reactionvessel of the cartridge of FIG. 1.

[0028]FIG. 22 is a front view of the vessel of FIG. 21.

[0029]FIG. 23 is a side view of the vessel of FIG. 21 inserted betweentwo heater plates.

[0030]FIG. 24 is a front view of one of the heater plates of FIG. 23.

[0031]FIG. 25 is a front view of an alternative reaction vesselaccording to the present invention.

[0032]FIG. 26 is a front view of another reaction vessel according tothe present invention.

[0033]FIG. 27 is another front view of the vessel of FIG. 21.

[0034]FIG. 28 is a front view of the vessel of FIG. 21 inserted into aheat-exchanging module of the instrument of FIG. 10.

[0035]FIG. 29 is an exploded view of a support structure for holding theplates of FIG. 23.

[0036] FIGS. 30-31 are assembled views of the support structure of FIG.29.

[0037]FIG. 32 is an isometric view showing the exterior of one theoptics assemblies in the heat-exchanging module of FIG. 28.

[0038]FIG. 33 is an isometric view of the plates of FIG. 23 in contactwith the optics assembly of FIG. 32.

[0039]FIG. 34 is a partially cut away, isometric view of the reactionvessel of FIG. 21 inserted between the plates of FIG. 23. only the lowerportion of the vessel is included in the figure.

[0040]FIG. 35 is a schematic block diagram of the electronics of theheat-exchanging module of FIG. 28.

[0041]FIG. 36 is an isometric view of an apparatus for disrupting cellsor viruses according to another embodiment of the invention.

[0042]FIG. 37 is a cross sectional view of the apparatus of FIG. 36.

[0043]FIG. 38 is an exploded view of a container used in the apparatusof FIG. 36.

[0044]FIG. 39 is a cross sectional view of the container of FIG. 38.

[0045]FIG. 40 is a schematic block diagram of a fluidic systemincorporating the apparatus of FIG. 36.

[0046]FIG. 41 is a cross sectional view of another container for use inthe apparatus of FIG. 36. An ultrasonic horn is in contact with a wallof the container that curves outwardly towards the horn.

[0047]FIG. 42 is a cross-sectional view of the wall of FIG. 41.

[0048] FIGS. 43A-43B are isometric views of opposite sides of anotherwall suitable for use in a container for holding cells or viruses to bedisrupted.

[0049]FIG. 44 is a partially cut-away, isometric view of a containerincorporating the wall of FIGS. 43A-43E;.

[0050]FIG. 45 is a bottom plan view of the container of FIG. 44.

DETAILED DESCRIPTION

[0051] The present invention provides an apparatus and method foranalyzing a fluid sample. In a first embodiment, the invention providesa cartridge for separating a desired analyte from a fluid sample and forholding the analyte for a chemical reaction. The fluid sample may be asolution or suspension. In a particular use, the sample may be a bodilyfluid (e.g., blood, urine, saliva, sputum, seminal fluid, spinal fluid,mucus, or other bodily fluids). Alternatively, the sample may be a solidmade soluble or suspended in a liquid or the sample may be anenvironmental sample such as ground or waste water, soil extracts,pesticide residues, or airborne spores placed in a fluid. Further, thesample may be mixed with one or more chemicals, reagents, diluents, orbuffers. The sample may be pretreated, for example, mixed withchemicals, centrifuged, pelleted, etc., or the sample may be in a rawform.

[0052] The desired analyte is typically intracellular material (e.g.,nucleic acid, proteins, carbohydrates, lipids, bacteria, orintracellular parasites). In a preferred use, the analyte is nucleicacid which the cartridge separates from the fluid sample and holds foramplification (e.g., using PCR) and optical detection. As used herein,the term “nucleic acid” refers to any synthetic or naturally occurringnucleic acid, such as DNA or RNA, in any possible configuration, i.e.,in the form of double-stranded nucleic acid, single-stranded nucleicacid, or any combination thereof.

[0053]FIG. 1 shows an isometric view of a cartridge 20 according to thepreferred embodiment. The cartridge 20 is designed to separate nucleicacid from a fluid sample and to hold the nucleic acid for amplificationand detection. The cartridge 20 has a body comprising a top piece 22, amiddle piece 24, and a bottom piece 26. An inlet port for introducing afluid sample into the cartridge is formed in the top piece 22 and sealedby a cap 30. Six pressure ports 32 are also formed in the top piece 22.The pressure ports 32 are for receiving nozzles from pressure sources,e.g., pumps or vacuums. The cartridge also includes alignment legs 28extending from the bottom piece 26 for positioning the cartridge 20 inan instrument (described below with reference to FIG. 10). Indentationsor depressions 38A, 38B, and 38C are formed in the top and middle pieces22, 24. The indentations are for receiving optical sensors that detectfluid flow in the cartridge 20. The cartridge 20 further includes vents34, 36. Each pressure port and vent preferably includes a hydrophobicmembrane that allows the passage of gas but not liquid into or out ofthe vents and pressure ports. Modified acrylic copolymer membranes arecommercially available from, e.g., Gelman Sciences (Ann Arbor, Mich.)and particle-track etched polycarbonate membranes are available fromPoretics, Inc. (Livermore, Calif.).

[0054]FIG. 2 is an isometric view showing the underside of the cartridge20. Nine holes 60 are formed in the bottom piece 26 for receiving valveactuators that open and close valves in the cartridge 20. A hole 62 isalso formed in the bottom piece 26 for receiving a transducer (describedin detail below with reference to FIG. 5). The cartridge 20 alsoincludes a reaction vessel 40 extending outwardly from the body of thecartridge. The vessel 40 has a reaction chamber 42 for holding areaction mixture (e.g., nucleic acid mixed with amplification reagentsand fluorescent probes) for chemical reaction and optical detection. Oneof the flow paths in the cartridge carries the reaction mixture to thechamber 42 for chemical reaction and optical detection. The vessel 40extends outwardly from the body of the cartridge 20 so that the vessel40 may be inserted between a pair of opposing thermal plates (forheating and cooling the chamber 42) without the need for decoupling thevessel 40 from the rest of the cartridge 20. This greatly reduces therisk of contamination and/or spilling. The vessel 40 may be integrallyformed with the body of the cartridge (e.g., integrally molded withmiddle piece 24). It is presently preferred, however, to produce thevessel 40 as a separate element that is coupled to the body duringmanufacture of the cartridge.

[0055] FIGS. 3-4 show exploded views of the cartridge. As shown in FIG.3, the middle piece 24 has multiple chambers formed therein. Inparticular, the middle piece 24 includes a sample chamber 65 for holdinga fluid sample introduced through the inlet port 64, a wash chamber 66for holding a wash solution, a reagent chamber 67 for holding a lysingreagent, a waste chamber 68 for receiving used sample and wash solution,a neutralizer chamber 70 for holding a neutralizer, and a master mixchamber 71 for holding a master mix (e.g., amplification reagents andfluorescent probes) and for mixing the reagents and probes with analyteseparated from the fluid sample. The sample chamber 65 optionallyincludes a side compartment 155 having slightly lower walls than thesample chamber 65. The side compartment 155 is for visually indicatingto a user when sufficient sample has been added to the sample chamber65, i.e., when the liquid level in the chamber 65 is high enough tospill over into the compartment 155.

[0056] The top piece 22 includes the vents 34, 36 and the six pressureports 32, as previously described. An elastomeric membrane or gasket 61is positioned and squeezed between the pieces 22, 24 to seal the variouschannels and chambers formed in the pieces. The middle piece 24preferably includes multiple sealing lips to ensure that the gasket 61forms an adequate seal. In particular, the middle piece 24 preferablyincludes sealing lips 73 surrounding each of the chambers 65, 66, 67,68. 70, and 71. The middle piece 24 also includes support walls 75around the perimeter, and intermediate sealing lips 76. The sealing lips73, 76 and support walls 75 locally compress the gasket 61 and achieve aseal.

[0057] As shown in FIG. 4, the middle piece 24 has formed in itsunderside various channels, one of which leads to a lysing chamber 86.The chamber 86 is aligned with the hole 62 in the bottom piece 26 sothat a transducer (e.g., an ultrasonic horn) may be inserted through thehole 62 to generate pressure waves in the lysing chamber 86. The middlepiece 24 also has nine valve seats 84 formed in its bottom surface. Thevalve seats 84 are aligned with the nine holes 60 in the bottom piece 26so that valve actuators may be inserted through the holes 60 into thevalve seats 84.

[0058] An elastomeric membrane or gasket 61 is positioned and squeezedbetween the pieces 24, 26 to seal the various channels, valve seats, andchamber formed in the middle piece 24. The middle piece 24 preferablyincludes multiple sealing lips to ensure that the gasket 63 forms anadequate seal. In particular, the middle piece 24 preferably includessealing lips 73 surrounding the lysing chamber 86, valve seats 84, andvarious channels. The middle piece 24 also includes support walls 75around its perimeter, and intermediate sealing lips 76. The sealing lips73, 76 and support walls 75 locally compress the gasket 63 and achieve aseal. In addition to sealing various channels and chambers, the gasket63 also functions as a valve stem by compressing, when actuated throughone of the holes 60, into a corresponding valve seat 84, thus shuttingone of the flow channels in the middle piece 24. This valve action isdiscussed in greater detail below with reference to FIGS. 15-16.

[0059] The gasket 63 also forms the bottom wall of the lysing chamber 86against which a transducer is placed to effect disruption of cells orviruses in the chamber 86. Each of the gaskets 61, 63 is preferablycomposed of an elastomer. Suitable gasket materials are silicone rubber,neoprene, EPDM, or any other compliant material. Each of the gaskets 61,63 preferably has a thickness in the range of 0.005 to 0.125 inches(0.125 to 3.175 mm), and more preferably in the range of 0.01 to 0.06inches (0.25 to 1.5 mm), with a presently preferred thickness of 0.031inches (0.79 mm). The thickness is selected to ensure that the gasket issufficiently compliant to seal the channels and chambers, to compressinto the valve seats 84 when forced, and to expand under pressure tocontact the transducer.

[0060] As shown in FIG. 3, the middle piece 24 includes a slot 79through which the reaction vessel 40 is inserted during assembly of thecartridge. The vessel 40 has two fluid ports 41, 43 for adding andremoving fluid from the vessel. When the top piece 22 is sealed to themiddle piece 24 via the gasket 61, the ports 41, 43 are placed intofluidic communication with channels 80, 81, respectively, that areformed in the top piece 22 (see FIG. 4). The gasket 61 seals therespective fluidic interfaces between the ports 41, 43 and the channels80, 81. The top, middle, and bottom pieces 22, 24, 26 are preferablyinjection molded parts made of a polymeric material such aspolypropylene, polycarbonate, or acrylic. Although molding is preferredfor mass production, it also possible to machine the top, middle, andbottom pieces 22, 24, 26. The pieces 22, 24, 26 may be held together byscrews or fasteners. Alternatively, ultrasonic bonding, solvent bonding,or snap fit designs could be used to assemble the cartridge.

[0061]FIG. 4 also shows a filter ring 88. The filter ring 88 compressesand holds a stack of filters in the lysing chamber 86. FIG. 6 shows anexploded view of a filter stack 87. The purpose of the filter stack 87is to capture cells or viruses from a fluid sample as the sample flowsthrough the lysing chamber 86. The captured cells or viruses are thendisrupted (lysed) in the chamber 86. The cells may be animal or plantcells, spores, bacteria, or microorganisms. The viruses may be any typeof infective agents having a protein coat surrounding an RNA or DNAcore.

[0062] The filter stack 87 comprises a gasket 93, a first filter 94, agasket 95, a second filter 97 having a smaller pore size than the firstfilter 94, a gasket 98, a third filter 100 having a smaller pore sizethan the second filter 97, a gasket 101, a woven mesh 102, and a gasket103. The filter stack also preferably includes a first set of beads 96disposed between the first and second filters 94 and 97 and a second setof beads 99 disposed between the second and third filters 97 and 100.The filter ring 88 compresses the filter stack 87 into the lysingchamber 86 so that the gasket 93 is pressed against the filter 94, thefilter 94 is pressed against the gasket 95, the gasket 95 is pressedagainst the filter 97, the filter 97 is pressed against the gasket 98,the gasket 98 is pressed against the filter 100, the filter 100 ispressed against the gasket 101, the gasket 101 is pressed against themesh 102, the mesh 102 is pressed against the gasket 103, and the gasket103 is pressed against the outer perimeter of the bottom wall of thelysing chamber 86. The gasket 95 is thicker than the average diameter ofthe beads 96 so that the beads are free to move in the space between thefilters 94 and 97. Similarly, the gasket 98 is thicker than the averagediameter of the beads 99 so that the beads 99 are free to move in thespace between the filters 97 and 100. A fluid sample flowing through thechannel 106 into the lysing chamber 86 first flows through filter 94,then through filter 97, next through filter 100, and lastly through themesh 102. After flowing through the filter stack 87, the sample flowsalong flow ribs 91 formed in the top of the lysing chamber 86 andthrough an outlet channel (not shown in FIG. 6).

[0063] Referring to FIG. 5, the cells or viruses captured in the filterstack (not shown in FIG. 5 for illustrative clarity) are lysed bycoupling a transducer 92 (e.g., an ultrasonic horn) directly to the wallof the lysing chamber 86. In this embodiment, the wall of the lysingchamber 86 is formed by the flexible gasket 63. The transducer 92 shoulddirectly contact an external surface of the wall. The term “externalsurface” is intended to mean a surface of the wall that is external tothe lysing chamber 86. The transducer 92 is a vibrating or oscillatingdevice that is activated to generate pressure waves in the chamber 86.The pressure waves agitate the beads 96, 99 (FIG. 6), and the movementof the beads ruptures the captured cells or viruses. In general, thetransducer for contacting the wall of the lysing chamber 86 may be anultrasonic, piezoelectric, magnetostrictive, or electrostatictransducer. The transducer may also be an electromagnetic device havinga wound coil, such, as a voice coil motor or a solenoid device. It ispresently preferred that the actuator be an ultrasonic transducer, suchas an ultrasonic horn. Suitable horns are commercially available fromtonics & Materials, Inc. having an office at 53 Church Hill, Newton,Connecticut 06470-1614 USA. Alternatively, the ultrasonic transducer maycomprise a piezoelectric disk or any other type of ultrasonic transducerthat may be coupled to the container. It is presently preferred to usean ultrasonic horn because the horn structure is highly resonant andprovides for repeatable and sharp frequency of excitation and largemotion of the horn tip.

[0064] As previously described in FIG. 6, the filter stack includes agasket at both of its ends. As shown in FIG. 5, the middle cartridgepiece 24 has a sealing lip 90 against which the gasket at one end of thefilter stack is compressed. The gasket at the other end of the filterstack is compressed by the filter ring 88 to form a seal. The gasketmaterial may expand into the relief area outside of the sealing lip 90.The width of the sealing lip 90 is small (typically 0.5 mm) so that anexcessive amount of force is not required to achieve a sufficient seal.

[0065] The filter ring 88 is held between the filter stack and thecartridge gasket 63. The cartridge gasket 63 is held between the middlepiece 24 and the bottom piece 26 by a sealing lip 406. Force istherefore transferred from the bottom piece 26 through the gasket 63 tothe filter ring 88 and finally to the filter stack. The filter ring 88contains a contact lip 404 that contacts the gasket 63. The contact lip404 is not a primary sealing lip (though it will seal) but a forcetransfer mechanism. The width of the contact lip 404 is larger than thewidth of the sealing lip 90 to ensure that deformation and sealingaction occurs in the filter stack and not taken up in squeezing thecartridge gasket 63. The cartridge middle piece 24 also has a sealinglip 406 that surrounds the filter ring 88. This is an active sealingarea that should not be compromised by the presence of the filter ring88. For this reason, there is a gap 407 between the sealing lip 406 andthe contact lip 404 on the filter ring 88. The gap 407 is provided toallow the gasket 63 to extrude into the gap 407 as it is compressed bythe sealing lip 406 and the contact lip 404. If the contact lip 404comes to a different elevation than the sealing lip 406, the seal willnot be compromised because of the gap 407 and the distance between thelips 404 and 406.

[0066] Referring again to FIG. 6, the filter stack 87 is effective forcapturing cells or viruses as a fluid sample flows through the stack 87without clogging of any of the filters 94, 97, 100 in the stack. Thefirst filter 94 (having the largest pore size) filters out coarsematerial such as salt crystals, cellular debris, hair, tissue, etc. Thesecond filter 97 (having the medium pore size) captures cells or virusesin the fluid sample. The third filter 100 (having the smallest poresize) captures smaller cells or viruses in the sample. The filter stack87 thus enables the simultaneous capture of differently sized samplecomponents without clogging of the filters. The average pore size of thefirst filter 94 is selected to be small enough to filter coarse materialfrom the fluid sample (e.g., salt crystals, cellular debris, hair,tissue) yet large enough to allow the passage of the target cells orviruses containing the desired analyte (e.g., nucleic acid or proteins).In general, the pore size of the first filter 94 should be in the rangeof about 2 to 25 μm, with a presently preferred pore size of about 5 μm.

[0067] The average pore sizes of the second and third filters areselected in dependence upon the average size of the target cells orviruses that contain the desired analyte(s). For example, in oneembodiment, the filter stack 87 is used to capture gonorrhea (GC) andchlamydia (Ct) organisms to determine the presence of the diseases inthe fluid sample. The GC and Ct: organisms have different averagediameters, about 1 to 2 μm for GC organisms and about 0.3 μm for Ctorganisms. In this embodiment, the second filter 97 has an average poresize of about 1.2 μm while the third filter 100 has an average pore sizeof about 0.22 μm so that most of the GC organisms are captured by thesecond filter 97 while most of the Ct organisms are captured by thethird filter 100. The filter stack thus enables the simultaneous captureof differently sized target organisms and does so without clogging ofthe filters. The pore sizes of the filters 97, 100 may be selected tocapture desired cells or viruses of any size, and the scope of theinvention is not limited to the specific example given.

[0068] The filter stack 87 is also useful for disrupting the capturedcells or viruses to release the intracellular material (e.g., nucleicacid) therefrom. The first and second sets of beads 96, 99 serve twouseful purposes in this regard. First, the beads are agitated by thepressure waves generated by the transducer. The movement of the beadsruptures the captured cells or viruses. Second, the beads may shear thenucleic acid released from the lysed cells or viruses so that thestrands of nucleic acid are sufficiently short to flow through thefilters and out of the lysing chamber 86. Suitable beads for rupturingcells or viruses include borosilicate glass, lime glass, silica, andpolystyrene beads.

[0069] The beads may be porous or non-porous and preferably have anaverage diameter in the range of 1 to 200 μm. The average diameter ofthe beads 96, 99 is selected in dependence upon the intended targetcells or viruses to be ruptured by the beads. The average diameter ofthe beads 96 in the first set may be equal to the average diameter ofthe beads 99 in the second set. Alternatively, when the first set ofbeads 96 is used to rupture a type of target cell or virus that differsfrom the type of cell or virus to be ruptured by the second set of beads99, it is advantageous to select the average diameter of the beads suchthat the average diameter of the beads 96 in the first set differs fromthe average diameter of the beads 99 in the second set. For example,when the filter stack is used to capture GC and Ct cells as describedabove, the beads 96 are 20 μm diameter borosilicate glass beads forrupturing the GC organisms and the beads 99 are 106 μm diameter sodalime glass beads for rupturing the Ct organisms. Each of the siliconegaskets 95, 98 should be sufficiently thick to allow room for the beads96, 99 to move and rupture the cells or viruses.

[0070] The mesh 102 also serves two useful purposes. First the meshprovides support to the filter stack 87. Second, the mesh breaks up airbubbles so that the bubbles can be channeled through the flow ribs 91and out of the lysing chamber 86. To effectively break up or reduce thesize of the air bubbles, the mesh 102 preferably has a small pore size.Preferably, it is a woven polypropylene mesh having an average pore sizeof about 25 μm. To ensure that the air bubbles can escape from thelysing chamber 86, it is desirable to use the cartridge in anorientation in which liquid flows up (relative to gravity) through thefilter stack 87 and the lysing chamber 86. The upward flow through thechamber 86 aids the flow of air bubbles out of the chamber 86. Thus, theinlet port for entry of fluids into the chamber 86 should generally beat the lowest point in the chamber, while the exit port should be at thehighest.

[0071] Many different embodiments of the filter stack are possible. Forexample, in one alternative embodiment, the filter stack has only twofilters and one set of beads disposed between the filters. The firstfilter has the largest pore size (e.g., 5 μm) and filters out coarsematerial such as salt crystals, cellular debris, hair, tissue, etc. Thesecond filter has a pore size smaller than the first filter and slightlysmaller than the target cells or viruses to be captured. Such a filterstack is described below with reference to FIG. 38. In anotherembodiment of the cartridge, the filter having the largest pore size(for filtering the coarse material) is positioned in a filter chamber(not shown) that is positioned upstream of the lysing chamber 86. Achannel connects the filter chamber to the lysing chamber 86. In thisembodiment, a fluid sample flows first through the coarse filter in thefilter chamber and then through a second filter in the lysing chamber totrap the target cells or viruses in the lysing chamber.

[0072] Further, the beads in the filter stack may have a bindingaffinity for target cells or viruses in the fluid sample to facilitatecapture of the target cells or viruses. For example, antibodies orcertain receptors may be coated onto the surface of the beads to bindtarget cells in the sample. Moreover, the lysing chamber 86 may containtwo different types of beads for interacting with target cells orviruses. For example, the lysing chamber may contain a first set ofbeads coated with antibodies or receptors for binding target cells orviruses and a second set of beads (intermixed with the first set) forrupturing the captured cells or viruses. The beads in the lysing chamber86 may also have a binding affinity for the intracellular material(e.g., nucleic acid) released from the ruptured cells or viruses. Suchbeads are useful for isolating target nucleic acid for subsequentelution and analysis. For example, the lysing chamber may contain silicabeads to isolate DNA or cellulose beads with oligo dT to isolatemessenger RNA for RT-PCR. The lysing chamber 86 may also contain beadsfor removing unwanted material (e.g., proteins, peptides) or chemicals(e.g., salts, metal ions, or detergents) from the sample that mightinhibit IPCR. For example, the chamber 86 may contain ion exchange beadsfor removing proteins. Alternatively beads having metal ion chelatorssuch as iminodiacetic acid will remove metal ions from biologicalsamples.

[0073] FIGS. 21-22 illustrate the reaction vessel 40 in greater detail.FIG. 21 shows a partially exploded view of the vessel 40, and FIG. 22shows a front view of the vessel 40. The vessel 40 includes the reactionchamber 42 (diamond-shaped in this embodiment) for holding a reactionmixture. The vessel 40 is designed for optimal heat transfer to and fromthe reaction mixture and for efficient optical viewing of the mixture.The thin shape of the vessel contributes to optimal thermal kinetics byproviding large surfaces for thermal conduction and for contactingthermal plates. In addition, the walls of the vessel provide opticalwindows into the chamber 42 so that the entire reaction mixture can beoptically interrogated. In more detail to FIGS. 21-22, the reactionvessel 40 includes a rigid frame 46 that defines the side walls 57A,57B, 59A, 59B of the reaction chamber 42. The frame 46 also defines aninlet port 41 and a channel 50 connecting the port 41 to the chamber 42.The frame 46 also defines an outlet port 43 and a channel 52 connectingthe port 43 to the chamber 42. The inlet port 41 and channel 50 are usedto add fluid to the chamber 42, and the channel 52 and outlet port 43are used for exit of fluid from the chamber 42. Alignment prongs 44A,44D are used to position the vessel 40 correctly during assembly of thecartridge.

[0074] As shown in FIG. 21, the vessel 40 also includes thin, flexiblesheets attached to opposite sides of the rigid frame 46 to form opposingmajor walls 48 of the chamber. (The major walls 48 are shown in FIG. 1exploded from the rigid frame 46 for illustrative clarity). The reactionchamber 42 is thus defined by the rigid side walls 57A, 57B, 59A, 59B ofthe frame 46 and by the opposing major walls 48. The opposing majorwalls 48 are sealed to opposite sides of the frame 46 such that the sidewalls 57A, 57B, 59A, 59B connect the major walls 48 to each other. Thewalls 48 facilitate optimal thermal conductance to the reaction mixturecontained in the chamber 42. Each of the walls 48 is sufficientlyflexible to contact and conform to a respective thermal surface, thusproviding for optimal thermal contact and heat transfer between thethermal surface and the reaction mixture contained in the chamber 42.Furthermore, the flexible walls 48 continue to conform to the thermalsurfaces if the shape of the surfaces changes due to thermal expansionor contraction during the course of the heat-exchanging operation.

[0075] As shown in FIG. 23, the thermal surfaces for contacting theflexible walls 48 are preferably formed by a pair of opposing plates190A, 190B positioned to receive the chamber 42 between them. When thechamber 42 of the vessel 40 is inserted between the plates 190A, 190DB,the inner surfaces of the plates contact the walls 48 and the flexiblewalls conform to the surfaces of the plates. The plates are preferablyspaced a distance from each other equal to the thickness T of thechamber 42 as defined by the thickness of the frame 46. In thisposition, minimal or no gaps are found between the plate surfaces andthe walls 48. The plates may be heated and cooled by various thermalelements to induce temperature changes within the chamber 42, as isdescribed in greater detail below.

[0076] The walls 48 are preferably flexible films of polymeric materialsuch as polypropylene, polyethylene, polyester, or other polymers. Thefilms may either be layered, e.g., laminates, or the films may behomogeneous. Layered films are preferred because they generally havebetter strength and structural integrity than homogeneous films. Inparticular, layered polypropylene films are presently preferred becausepolypropylene is not inhibitory to PCR. Alternatively, the walls 48 maycomprise any other material that may be formed into a thin, flexiblesheet and that permits rapid heat transfer. For good thermalconductance, the thickness of each wall 48 is preferably between about0.003 to 0.5 mm, more preferably between 0.01 to 0.15 mm, and mostpreferably between 0.025 to 0.08 mm.

[0077] Referring again to FIG. 22, the vessel 40 also preferablyincludes optical windows for in situ optical interrogation of thereaction mixture in the chamber 42. In the preferred embodiment, theoptical windows are the side walls 57A, 57B of the rigid frame 46. Theside walls 57A, 57B are optically transmissive to permit excitation ofthe reaction mixture in the chamber 42 through the side wall 57A anddetection of light emitted from the chamber 42 through the side wall57B. Arrows A represent illumination beams entering the chamber 42through the side wall 57A and arrows B represent emitted light (e.g.,fluorescent emission from labeled analytes in the reaction mixture)exiting the chamber 42 through the side wall 57B.

[0078] The side walls 57A, 57B are preferably angularly offset from eachother. It is usually preferred that the walls 57A, 57B are offset fromeach other by an angle of about 90°. A 90° angle between excitation anddetection paths assures that a minimum amount of excitation radiationentering through the wall 57A will exit through wall 57B. In addition,the 90° angle permits a maximum amount of emitted light (e.g.fluorescence) to be collected through wall 57B. The walls 57A, 57B arepreferably joined to each other to form a “V” shaped intersection at thebottom of the chamber 42. Alternatively, the angled walls 57A, 57B neednot be directly joined to each other, but may be separated by anintermediary portion, such as another wall or various mechanical orfluidic features which do not interfere with the thermal and opticalperformance of the vessel. For example, the walls 57A, 57B may meet at aport which leads to another processing area in communication with thechamber 42, such as an integrated capillary electrophoresis area. In thepresently preferred embodiment, a locating tab 58 extends from the Frame46 below the intersection of walls 57A, 57B. The tab 58 is used toproperly position the vessel 40 in a heat-exchanging module describedbelow with reference to FIG. 28.

[0079] Optimum optical sensitivity may be attained by maximizing theoptical path length of the light beams exciting the labeled analyte inthe reaction mixture and the emitted light that is detected, asrepresented by the equation:

I _(o) /I _(i) =C*L*A,

[0080] where I_(o) is the illumination output of the emitted light involts, photons or the like, C is the concentration of analyte to bedetected, I_(i) is the input illumination, L is the path length, and Ais the intrinsic absorptivity of the dye used to label the analyte.

[0081] The thin, flat reaction vessel 40 of the present inventionoptimizes detection sensitivity by providing maximum optical path lengthper unit analyte volume. Referring to FIGS. 23 and 27, the vessel 40 ispreferably constructed such that each of the sides walls 57A, 57B, 59A,59B of the chamber 42 has a length L in the range of 1 to 15 mm, thechamber has a width W in the range of 1.4 to 20 mm, the chamber has athickness T in the range of 0.5 to 5 mm, and the ratio of the width W ofthe chamber to the thickness T of the chamber is at least 2:1. Theseparameters are presently preferred to provide a vessel having arelatively large average optical path length through the chamber, i.e. 1to 15 mm on average, while still keeping the chamber sufficiently thinto allow for extremely rapid heating and cooling of the reaction mixturecontained therein. The average optical path length of the chamber 42 isthe distance from the center of the side wall 57A to the center of thechamber 42 plus the distance from the center of the chamber 42 to thecenter of the side wall 57B.

[0082] More preferably, the vessel 40 is constructed such that each ofthe sides walls 57A, 57B, 59A, 59B of the chamber 42 has a length L inthe range of 5 to 12 mm, the chamber has a width W in the range of 7 to17 mm, the chamber has a thickness T in the range of 0.5 to 2 mm, andthe ratio of the width W of the chamber to the thickness T of thechamber is at least 4:1. These ranges are more preferable because theyprovide a vessel having both a larger average optical path length (i.e.,5 to 12 mm) and a volume capacity in the range of 12 to 100 μl whilestill maintaining a chamber sufficiently thin to permit extremely rapidheating and cooling of a reaction mixture. The relatively large volumecapacity provides for increased sensitivity in the detection of lowconcentration analytes, such as nucleic acids.

[0083] In the preferred embodiment, the reaction vessel 40 has adiamond-shaped chamber 42 defined by the side walls 57A, 57B, 59A, 59B,each of the side walls has a length of about 10 mm, the chamber has awidth of about 14 mm, the chamber has a thickness T of 1 mm as definedby the thickness of the frame 46, and the chamber has a volume capacityof about 100 μl. This reaction vessel provides a relatively largeaverage optical path length of 10 mm through the chamber 42.Additionally, the thin chamber allows for extremely rapid heating and/orcooling of the reaction mixture contained therein. The diamond-shape ofthe chamber 42 helps prevent air bubbles from forming in the chamber asit is filled with the reaction mixture and also aids in opticalinterrogation of the mixture.

[0084] Referring again to FIG. 22, the frame 46 is preferably made of anoptically transmissive material, e.g., a polycarbonate or clarifiedpolypropylene, so that the side walls 57A, 57B are opticallytransmissive. As used herein, the term optically transmissive means thatone or more wavelengths of light may be transmitted through the walls.In the preferred embodiment, the optically transmissive walls 57A, 57Bare substantially transparent. In addition, one or more optical elementsmay be present on the optically transmissive side walls 57A, 57B. Theoptical elements may be designed, for example, to maximize the totalvolume of solution which is illuminated by a light source, to focusexcitation light on a specific region of the chamber 42, or to collectas much fluorescence signal from as large a fraction of the chambervolume as possible. In alternative embodiments, the optical elements maycomprise gratings for selecting specific wavelengths, filters forallowing only certain wavelengths to pass, or colored lenses to providefiltering functions. The wall surfaces may be coated or comprisematerials such as liquid crystal for augmenting the absorption ofcertain wavelengths. In the presently preferred embodiment, theoptically transmissive walls 57A, 57B are substantially clear, flatwindows having a thickness of about 1 mm.

[0085] The side walls 59A, 59B preferably includes reflective faces 56which internally reflect light trying to exit the chamber 42 through theside walls 59A, 59B. The reflective faces 56 are arranged such thatadjacent faces are angularly offset from each other by about 90°. Inaddition, the frame 46 defines open spaces between the side walls 59A,59B and the support ribs 53. The open spaces are occupied by ambient airthat has a different refractive index than the material composing theframe (e.g., plastic). Due to the difference in the refractive indexes,the reflective faces 56 are effective for internally reflecting lighttrying to exit the chamber through the walls 59A, 59B and provide forincreased detection of optical signal through the walls 57A, 57B.Preferably, the optically transmissive side walls 57A, 57B define thebottom portion of the diamond-shaped chamber 42, and theretro-reflective side walls 59A, 59B define the top portion of thechamber.

[0086] A preferred method for fabricating the reaction vessel 40 willnow be described with reference to FIGS. 21-22. The reaction vessel 40may be fabricated by first molding the rigid frame 46 using knowninjection molding techniques. The frame 46 is preferably molded as asingle piece of polymeric material, e.g., clarified polypropylene. Afterthe frame 46 is produced, thin, flexible sheets are cut to size andsealed to opposite sides of the frame 46 to form the major walls 48 ofthe chamber 42. The major walls 48 are preferably cast or extruded filmsof polymeric material, e.g., polypropylene films, that are cut to sizeand attached to the frame 46 using the following procedure. A firstpiece of film is placed over one side of the frame 46. The frame 46preferably includes a tack bar 47 for aligning the top edge of the film.The film is placed over the bottom portion of the frame 46 such that thetop edge of the film is aligned with the tack bar 47 and such that thefilm completely covers the bottom portion of the frame 46 below the tackbar 47. The film should be larger than the bottom portion of the frame46 so that it may be easily held and stretched flat across the frame.The film is then cut to size to match the outline of the frame byclamping to the frame the portion of the film that covers the frame andcutting away the portions of the film that extend past the perimeter ofthe frame using, e.g., a laser or die. The film is then tack welded tothe frame, preferably using a laser.

[0087] The film is then sealed to the frame 46, preferably by heatsealing. Heat sealing is presently preferred because it produces astrong seal without introducing potential contaminants to the vessel asthe use of adhesive or solvent bonding techniques might do. Heat sealingis also simple and inexpensive. The heat sealing may be performed using,e.g., a heated platen. An identical procedure may be used to cut andseal a second sheet to the opposite side of the frame 46 to complete thechamber 42. Many variations to this fabrication procedure are possible.For example, in an alternative embodiment, the film is stretched acrossthe bottom portion of the frame 46 and then sealed to the frame prior tocutting the film to size. After sealing the film to the frame, theportions of the film that extend past the perimeter of the frame are cutaway using, e.g., a laser or die.

[0088] Although it is presently preferred to mold the frame 46 as asingle piece, it is also possible to fabricate the frame from multiplepieces. For example, the side walls 57A, 57B forming the angled opticalwindows may be molded from polycarbonate, which has good opticaltransparency, while the rest of the frame is molded from polypropylene,which is inexpensive and compatible with PCR. The separate pieces can beattached together in a secondary step. For example, the side walls 57A,57B may be press-fitted and/or bonded to the remaining portion of theframe 46. The flexible walls 48 may then be attached to opposite sidesof the frame 46 as previously described.

[0089] Referring again to FIG. 3, it is presently preferred to use agasket 61 to seal the ports 41, 43 of the vessel 40 to correspondingchannels 80, 81 (FIG. 4) in the cartridge body. Alternatively, fluidicseals may be established using a luer fitting, compression fitting, orswaged fitting. In another embodiment, the cartridge body and frame ofthe vessel 40 are molded as a single part, and the flexible major wallsof the vessel are heat-sealed to opposite sides of the frame.

[0090] Referring again to FIG. 22, the chamber 42 is filled by forcingliquid (e.g., a reaction mixture) to flow through the port 41 and thechannel 50 into the chamber 42. The liquid may be forced to flow intothe chamber 42 using differential pressure (i.e., either pushing theliquid through the inlet port 41 or aspirating the liquid by applying avacuum to the outlet port 43). As the liquid fills the chamber 42, itdisplaces air in the chamber. The displaced air exits the chamber 42through the channel 52 and the port 43. For optimal detection of analytein the chamber 42, the chamber should not contain air bubbles. To helpprevent the trapping of air bubbles in the chamber 42, the connectionbetween the chamber 42 and the outlet channel 52 should be at thehighest point (with respect to gravity) in the chamber 42. This allowsair bubbles in the chamber 42 to escape without being trapped. Thus, thevessel 40 is designed to be used in the vertical orientation shown inFIG. 22.

[0091]FIG. 25 shows another vessel 206 designed to be used in ahorizontal orientation. The vessel 206 has an inlet port 41 and an inletchannel 50 connecting the inlet port 41 to the bottom of the chamber 42.The vessel also has an outlet port 43 and an outlet channel 50connecting the outlet port 43 to the top of the chamber 42. Thus, anyair bubbles in the chamber 42 may escape through the outlet channel 52without becoming trapped. FIG. 26 shows another vessel 207 having twoinlet ports 41, 45 and one outlet port 43. Inlet channels 50, 54 connectthe respective inlet ports 41, 45 to the chamber 42, and outlet. channel52 connects the chamber 42 to outlet port 43. Many other differentembodiments of the vessel are also possible. In each embodiment, it isdesirable to evacuate the chamber 42 from the highest point (withrespect to gravity) in the chamber and to introduce liquid into thechamber from a lower point.

[0092] FIGS. 15A-15B illustrate two types of valves used in thecartridge. As shown in FIG. 15A, there are two types of fundamentalconcepts to the valve action, and hence two types of valves. The firstvalve uses a cone-shaped or conical valve seat 160 formed in the middlecartridge piece 24. The valve seat 160 is a depression, recess, orcavity molded or machined in the middle piece 24. The valve seat 160 isin fluid communication with a chamber 167 through a port or channel 157that intersects the center of the conical valve seat 160. As shown inFIG. 15B, a valve actuator 164 having a spherical surface is forcedagainst the elastic membrane 63 and into the valve seat 160,establishing a circular ring of contact between the membrane 63 and thevalve seat 160. The kinematic principle is that of a ball seated into acone. The circular seal formed by the membrane 63 and valve seat 160prevents flow between the channel 157 (and hence the chamber 167) and aside channel 158 extending from a side of the valve seat 160. The sidechannel 158 is defined by the membrane 63 and the middle cartridge piece24.

[0093] As shown in FIG. 15A, the other type of valve controls the crossflow between the channel 158 and another side channel 159 formed betweenthe membrane 63 and the middle cartridge piece 24. In this case, acircular ring of contact would be ineffective. Instead, the second valvecomprises a recess depression or cavity 161 formed in the middlecartridge piece 24. The cavity 161 separates the channels 158, 159 fromeach other. An end of the channel 158 is positioned on one side of thecavity 161, and an end of the channel 159 is positioned on the oppositeside of the cavity 161. The cavity 161 is defined by a first, curvedsurface 162A positioned adjacent the end of the channel 158, a secondcurved surface 162B positioned adjacent the end of the channel 159, anda third surface 163 between the first and second curved surfaces 162A,162B. As shown in FIG. 15B, the curved surfaces provide two valve seatsthat are the primary contact area for the membrane 63 to seal off theflow between the channels 158 and 159. The kinematic principle is thatof a ball (or spherical end on a valve actuator) held by three contactpoints, the upward force on the actuator and the two valve seats 162A,162B.

[0094] As shown in FIG. 16A, the first and second curved surfaces 162A,162B are preferably concentric spherical surfaces. The valve actuator164 has also has a spherical surface for pressing the membrane 63tightly against the surfaces 162A, 162B. In addition, each of thesurfaces 162A, 162B preferably has a spherical radius of curvature R1equal to the combined radius of curvature R2 of the valve actuator 164plus the thickness T of the membrane 63.

[0095] For example, if the radius of curvature R2 of the surface of thevalve actuator 164 is 0.094 inches and the membrane 63 has a thickness Tof 0.031 inches, then the radius of curvature R1 of each of the surfaces162A, 162B is 0.125 inches. In general, the size and radius of curvatureof the valve seats is dependent upon the size of the channels in thecartridge. The valves are preferably made just large enough toeffectively seal the channels but no larger so that dead volume in thecartridge is minimized.

[0096] As shown in FIG. 16B, the third surface 163 is recessed from thefirst and second surfaces 162A, 162B to provide a gap 166 between themembrane 63 and the third surface 163 when the membrane 63 is pressedagainst the first and second surfaces 162A, 162B. Stated another way,the surfaces 162A, 162B are raised or elevated from the surface 163. Thegap 166 ensures that the membrane 63 contacts primarily the valve seats162A, 162B rather than the entire surface of the cavity 161 so thatmaximum pressure is applied to the valve seats 162A and 162B by themembrane 63. This provides a very strong seal with minimal actuatorforce required.

[0097] Referring again to FIG. 15B, in both types of valves therespective kinematic principle defines the location of the mating parts.In both the ball-in-cone concept and theball-against-two-spherical-surfaces concept, the ball or sphericalshaped valve actuator is permitted to seek its own location as it isforced against the valve seat(s). There is a deliberate clearance (e.g.,0.01 to 0.03 inches) between the valve actuator and the hole in thebottom cartridge piece 26 in which the actuator 164 travels so that onlythe valve seat action defines the location of the mating pieces.

[0098] The valve actuators can be controlled by a variety of mechanisms.FIGS. 17-19 illustrate one such mechanism. As shown in FIG. 17, a valveactuator 172 has a spherical surface for pressing the gasket 63 into avalve seat. The actuator 172 also has a flange 177 on its bottomportion. The cartridge includes an elastic body, such as a spring 174,that pushes against a ledge in the lower cartridge piece 26 to bias thevalve actuator against the gasket 63. The spring 174 is sufficientlystrong to close the valve unless a deliberate force is applied to pulldown the actuator 172. The valves in the cartridge may be kept closed inthis manner for shipping and storage before the cartridge is used. Thus,the cartridge may be preloaded during manufacture with the necessaryreagents and wash solutions to analyze a fluid sample without the fluidsleaking out of the cartridge during shipping and storage.

[0099] The actuator pull-down mechanism is usually located in aninstrument into which the cartridge is placed for sample analysis (onesuch instrument is described in detail below with reference to FIG. 10).The mechanism comprises a sliding guide 175 that rotates a hingedpull-down member 180 having a jaw 181 for receiving the flange 177 ofthe actuator 172. As shown in FIG. 18, the sliding guide 175 rotates thehinged pull-down member 180 until the flange 177 is positioned withinthe jaw 181. As shown in FIG. 19, a solenoid 146 pulls down the member180 and thus the valve actuator 172 so that the gasket 63 is releasedfrom the valve seat, thus opening the valve and permitting fluid flowbetween the channels 170 and 171.

[0100]FIG. 20 illustrates the manner in which fluid flow into and out ofthe sample chamber, wash chamber, neutralizer chamber, and reagentchambers is controlled in the cartridge. Each of these chambers, asillustrated by a chamber 414 in FIG. 20, is covered by a hydrophobicmembrane 410 that allows the passage of gas but not liquid therethrough.The hydrophobic membrane 410 is positioned between the chamber 414 and apressure port 32. The pressure port 32 is formed in the upper cartridgepiece 22 and positioned over the chamber 414. The membrane 410 holdsliquids in the chamber 414 during shipping and storage of the cartridge,even if the cartridge is turned upside down. The pressure port 32 issized to receive a pressure nozzle 182 that is connected to a pressuresource (e.g., a vacuum or pneumatic pump) usually located in theexternal instrument. The nozzle 182 includes an o-ring 184 and a flange415. A spring 185 pushes against the flange 415 to force the nozzle 182into the pressure port 32 so that the o-ring 184 establishes a sealaround the port 32. In operation, positive air pressure or a vacuum isapplied to the chamber 414 through the pressure port 32 to force liquidsout of or into, respectively, the chamber 414.

[0101] A conical valve seat 160 (previously described with reference toFIGS. 15A-15B) is formed in the middle cartridge piece 24 below thechamber 414 to control the flow of liquid between the chamber 414 and aconnecting channel 411. The valve is opened and closed by a valveactuator 188 having a flange 187 and a spring 188 pressing against theflange to hold the valve closed until a downward force is applied to theactuator 186. The downward force is preferably supplied by a solenoidthat pulls down the actuator 186 to open the valve. The valve actuator186 and solenoid are preferably located in the instrument.

[0102] FIGS. 7-8 show top and bottom plan views, respectively, of thecartridge. FIG. 9 is a schematic block diagram of the cartridge. Asshown in any of FIGS. 7-9, the cartridge includes a sample chamber 65having a port for adding a fluid sample to the cartridge and a sampleflow path extending from the sample chamber 65. The sample flow pathextends from the sample chamber 65 through a valve 107 and into achannel 106. The channel 106 includes a sensor region 136 in which thechannel 106 has a flat bottom enabling easy optical detection of thepresence of liquid in the channel. The sample flow path continues fromthe channel 106 into the lysing chamber 86 and through the filter stack87. The sample flow path also includes a channel 109 for exit of fluidfrom the lysing chamber 86, a channel 110 having a flat-bottomeddetection region 137, a valve 111, and a channel 112 leading to thevented waste chamber 68 through a valve 114.

[0103] The cartridge also includes the wash chamber 66 for holding washsolution and the reagent chamber 67 for holding lysing reagent. The washchamber 66 is connected to the lysing chamber 86 through a valve 115,channel 117, and channel 106. The reagent chamber 67 is connected to thelysing chamber 86 through a valve 119, channel 117, and channel 106.Sample components (e.g., cells or viruses in the sample) are captured inthe filter stack 87 and lysed in the chamber 86 to release targetanalyte (e.g., nucleic acid) from the sample components. The cartridgealso includes an analyte flow path extending from the lysing chamber 86for carrying the analyte separated from the fluid sample to the reactionvessel 40 for chemical reaction and optical detection. The analyte flowpath extends from the chamber 86 through the channel 109, channel 110,and valve 111. After passing through the valve 111, the analyte flowpath diverges from the sample flow path. While the sample flow pathextends though channel 112 into the waste chamber 68, the analyte flowpath diverges into the U-shaped channel 122. The analyte flow path thenextends into and out of the neutralizer chamber 70 through a valve 124.The analyte flow path also passes into and out of the master mix chamber71 through a valve 126. From the master mix chamber 71, the analyte flowpath extends along the channel L22, through a valve 127, through channel80, and into the reaction vessel 40 through the port 41.

[0104] The reaction vessel 40 includes the port 41 for adding a reactionmixture to the vessel, and the port 43 for exit of fluids (e.g., air orexcess reaction mixture) from the vessel. The cartridge also includeschannel 81 in fluid communication with the port 43. The channel 81includes a flat-bottomed detection region 130 for detecting the presenceof liquid in the channel. The channel 81 connects to a channel 131(channel 131 extends straight down perpendicular to the page in the topplan view of FIG. 7). Channel 131 connects to a channel 132 which inturn connects to a channel 134 through a valve 133 (channel 134 extendsstraight up perpendicular to the page in the top plan view of FIG. 7).The channel 134 leads to the vent 36 which has a hydrophobic membrane topermit the escape of gas but not liquid from the cartridge. Thechannels, vent and valve positioned downstream from the reaction vessel40 are used to pressurize the chamber 42 of the vessel, as is describedin the operation section below.

[0105] The cartridge also includes a first pressure port 105 positionedabove the sample chamber 65, a second pressure port 116 positioned abovethe wash chamber 66, a third pressure port 118 positioned above thereagent chamber 67, a fourth pressure port 123 positioned above theneutralizer chamber 70, a fifth pressure port 125 positioned above themaster mix chamber 71, and a sixth pressure port 128 positioned at theend of the U-shaped channel 122. The cartridge further includes sensorchambers 120 and 121 in fluid communication with the waste chamber 68.The sensor chambers 120 and 121 indicate when predetermined volumes ofliquid have been received in the waste chamber 68, as is described indetail below.

[0106] Referring to FIG. 10, the cartridge is preferably used incombination with an instrument 140 designed to accept one or more of thecartridges. For clarity of illustration, the instrument 140 shown inFIG. 10 accepts just one cartridge. It is to be understood, however,that the instrument may be designed to process multiple cartridgessimultaneously. The instrument 140 includes a cartridge nest 141 intowhich the cartridge is placed for processing. The instrument 140 alsoincludes the transducer 92 (e.g., an ultrasonic horn) for generatingpressure waves in the lysing chamber of the cartridge, nine valveactuators 142 for actuating the nine valves in the cartridge, ninecorresponding solenoids 146 for pulling down the valve actuators, andsix ispressure nozzles 145 for interfacing with six correspondingpressure ports formed in the cartridge. In addition, the instrumentincludes or is connected to one or more regulated pressure sources forsupplying pressure to the cartridge through the pressure nozzles 145.Suitable pressure sources include syringe pumps, compressed air sources,pneumatic pumps, or connections to external sources of pressure. Theinstrument further includes three slotted optical sensors 143 and threereflective optical sensors 144.

[0107]FIG. 13 illustrates the slotted optical sensors 143 positioned todetect liquid in the sensor chambers 120, 121 and in the reagent chamber67. Each sensor 143 includes a built in LED and photodiode positioned onopposite sides of the sensor. The LED emits a beam that is detected bythe photodiode if the beam is not substantially refracted. Such slottedoptical sensors are commercially available from a number of suppliers.The cartridge is shaped so that the slotted optical sensors fit aroundthe chambers 67, 120, and 121. The operation of each sensor is asfollows. If liquid is not present in the chamber the sensor surrounds,the beam from the LED is substantially refracted by air in the chamberand the curved inner walls of the chamber and only a weak signal, ifany, is detected by the photodiode since air has an index of refractionthat does not closely match that of the plastic cartridge. If there isliquid present in the chamber, however, the beam from the LED does notrefract or is only slightly refracted and produces a much strongersignal detected by the photodiode since the liquid has an index ofrefraction closely matching that of the plastic cartridge. The opticalsensors 143 are therefore useful for determining the presence or absenceof liquid in the chambers 67, 120, and 121.

[0108]FIG. 14 shows a cut-away, schematic side view of the sensorchamber 120 in fluid communication with the waste chamber 68 andsurrounded by the slotted optical sensor 143. The sensor chamber 120 andsensor 143 are used to indicate when a predetermined volume of liquid ispresent in the waste chamber 68. The sensor chamber 120 is partiallyseparated from the waste chamber 68 by a wall 151 having a spillover rim152. The height of the wall is selected so that when the predeterminedvolume of liquid is received in the waste chamber 68, the liquid spillsover the spillover rim 152 and into the sensor chamber 120. The liquidin the sensor chamber 120 is then detected by the sensor 143.

[0109] Referring again to FIG. 13, the cartridge may also include asecond sensor chamber 121 in fluid communication with the waste chamber68. The second sensor chamber 121 is also separated from the wastechamber 68 by a wall 153 having a spillover rim. The wall 153 is tallerthan the wall 152 so that liquid does not spill over the wall 153 untila second predetermined volume of fluid in addition to the firstpredetermined volume of fluid has been received in the waste chamber 68.The sensor chambers 120, 121 and the optical sensors 143 are useful forcontrolling the operation of the cartridge. The height of the wall 152is preferably selected such that when a fixed volume of fluid samplefrom the sample chamber 65 has flowed through the sample flow path tothe waste chamber 68, the sample liquid spills over into the sensorchamber 120 and is detected. The detection in chamber 120 triggers therelease of wash solution from the wash chamber 66 which flows throughthe sample flow path to the waste chamber 68. When an incremental volumeof the wash solution is received in the chamber 68, liquid spills overthe wall 153 into the sensor chamber 121 and is detected. The detectionof liquid in the chamber 121 then triggers the release of lysing reagentfrom the chamber 67. The sensor 143 surrounding the chamber 67 may thenbe used to indicate when the chamber 67 is empty, triggering the startof ultrasonic lysis. In an alternative embodiment, the cartridge mayhave two waste chambers, one for sample and one for wash, with eachwaste chamber having a respective sensor chamber connected thereto.

[0110] In-line reflective optical sensors 144 are used to determine thepresence or absence of liquid in the flat-bottomed detection regions130, 136, 137, of channels 81, 106, and 110, respectively (FIG. 7). Eachsensor 144 has a built in emitter and detector that is positioned over aflat-bottomed detection region. The emitter emits a beam that isreflected from the cartridge and detected by the detector. The sensordetects a change in signal when as an air/liquid interface passesthrough the detection region. Optionally, dual emitter reflectiveoptical sensors may be used for a more reliable detection operation.Both types of reflective optical sensors are well known in the art andcommercially available.

[0111] Referring again to FIG. 10, the instrument 140 also includes aheat-exchanging module 147 having a slot 148 for receiving the reactionvessel of the cartridge. The module 147 is described in detail belowwith reference to FIG. 28. The instrument 140 further includes a latchmechanism 149 for latching a lid 150 over a cartridge. The cartridgenest 141 includes alignment holes 401 for receiving the legs of thecartridge. The alignment holes 401 ensure proper positioning of thecartridge in the nest 141 so that the pressure nozzles 145, transducer92, and valve actuators 142 fit into the corresponding ports in thecartridge and so that the reaction vessel fits into the slot 148. Thetransducer 92 should be positioned in the instrument 140 such that whenthe cartridge is placed in the nest 141, the transducer contacts thebottom wall of the lysing chamber 86, as shown in the cut-away view ofFIG. 5. In addition, the instrument may include a spring or similarmechanism to bias the transducer 92 against the wall of the lysingchamber 86.

[0112] The instrument 140 also includes various conventional equipmentnot shown in FIG. 10 including a main logic board having amicrocontroller for controlling the operation of the solenoids 146,transducer 92, heat-exchanging module 147, and optical sensors 143, 144.The instrument also includes or is connected to a power supply forpowering the instrument and a pneumatic pump for supplying air pressurethrough the nozzles 145. The instrument 140 is preferablycomputer-controlled using, e.g., the microcontroller which is programmedto perform the functions described in the operation section below.Alternatively, the instrument may controlled by a separate computer, orcontrolled by a combination of a separate computer and an on-boardmicrocontroller.

[0113]FIG. 11 shows an isometric view of the cartridge 20 placed in theinstrument 140 for processing. FIG. 11 shows a partial cut-away view ofthe instrument 140 with the lid 150 closed. Referring again to FIG. 11,a memory or microprocessor chip may optionally be incorporated as partof the cartridge 20. This chip preferably contains information such asthe type of cartridge, program information such as specific protocolsfor the processing of the cartridge, tolerances for accept and reject,serial numbers and lot codes for quality tracking, and provision forstoring the results of the processing. Integrated electronic memory onthe cartridge 20 allows for rapid, easy, and error-free set-up of theinstrument 140 for different fluidic processing protocols. When thecartridge 20 is inserted into the instrument 140, the instrument mayelectronically address the memory on the cartridge, and thusautomatically receive the appropriate set of instructions forcontrolling the time-sequence of fluidic operations to be carried outwith the inserted cartridge. The instrument 140 may simply sequentiallyretrieve and execute each step in the cartridge's memory, or downloadits contents so that the user may edit the sequence using, e.g., thecontroller computer.

[0114] If suitable memory is included on the cartridge, such as writablememory (e.g., erasable programmable read-only memory (EPROM),electrically erasable programmable read-only memory (EEPROM), etc.,intermediate and final results, based on the sample introduced into thecartridge, could be written by the instrument into the cartridge'smemory for co-located storage with the physical sample after processing.This is particularly advantageous in applications where archiving ofsamples and results is necessary, such as forensics. In addition, otherinformation can be stored in the memory on the cartridge, in unalterable(or alterable) forms. For example, cartridge serial number, lotmanufacture information, and related information could be pre-programmedand unalterable. User data, technician identification number, date oftest, location of test and instrument serial number could be unalterablywritten into the cartridge. This allows for easy identification of the“chain of custody” in the handling of a specimen. Engineers skilled inthe art of data storage will recognize that other memory means thanelectronic can be used, such as optically-addressed printed regions(e.g., ink-jet or thermal), magnetic strips, etc.

[0115]FIG. 28 shows the heat-exchanging module 147 of the instrumentinto which the reaction vessel 40 is inserted for thermal processing andoptical detection of target analyte(s) in the reaction mixture. Themodule 147 preferably includes a housing 208 for holding the variouscomponents of the module. The module 147 also includes the thermalplates 190 described above. The housing 208 includes a slot (not shownin FIG. 28) above the plates 190 so that the reaction chamber of thevessel 40 may be inserted through the slot and between the plates. Theheat-exchanging module 147 also preferably includes a cooling system,such as a fan 212. The fan 212 is positioned to blow cooling air pastthe surfaces of the plates 190 to cool the plates and hence cool thereaction mixture in the vessel 40. The housing 208 preferably defineschannels for directing the cooling air past the plates 190 and out ofthe module 147.

[0116] The heat-exchanging module 147 further includes an opticalexcitation assembly 216 and an optical detection assembly 218 foroptically interrogating the reaction mixture contained in the vessel 40.The excitation assembly 216 includes a first circuit board 220 forholding its electronic components, and the detection assembly 216includes a second circuit board 222 for holding its electroniccomponents. The excitation assembly 216 includes one or more lightsources (e.g., an LED). laser, or light bulb) for excitingfluorescently-labeled analytes in the vessel 40. The excitation assembly216 also includes one or more lenses for collimating the light from thelight sources, as well as filters for selecting the excitationwavelength ranges of interest. The detection assembly 218 includes oneor more detectors (e.g., a photodiode, photomultiplier tube, or CCD) fordetecting the light emitted from the vessel 40. The detection assembly218 also includes one or more lenses for focusing and collimating theemitted light, as well as filters for selecting the emission wavelengthranges of interest. Suitable optical excitation and detection assembliesfor use in the heat-exchanging module 147 are described in InternationalPublication Number WO 99/60380 (International Application NumberPCT/US99/11182) published Nov. 25, 1999, the disclosure of which isincorporated by reference herein.

[0117] The optics assemblies 216, 218 are positioned in the housing 208such that when the chamber of the vessel 40 is inserted between theplates 190, the excitation assembly 216 is in optical communication withthe chamber 42 through the optically transmissive side wall 57A (seeFIG. 22) and the detection assembly 218 is in optical communication withthe chamber through the optically transmissive side wall 57B (FIG. 22).In the preferred embodiment, the optics assemblies 216, 218 are placedinto optical communication with the optically transmissive side walls bysimply locating the optics assemblies 216, 218 next to the bottom edgesof the plates 190 so that when the chamber of the vessel is placedbetween the plates, the optics assemblies 216, 218 directly contact, orare in close proximity to, the side walls.

[0118]FIG. 34 shows a partially cut-away, isometric view of the chamberof the vessel inserted between the plates 190A, 190B (the top portion ofthe vessel is cut away). The vessel preferably has an angled bottomportion (e.g., triangular) formed by the optically transmissive sidewalls 57A, 57B. Each of the plates 190A, 190B has a correspondinglyshaped bottom portion. The bottom portion of the first plate 190A has afirst bottom edge 250A and a second bottom edge 2190B. Similarly, thebottom portion of the second plate 190B has a first bottom edge 252A anda second bottom edge 252B. The first and second bottom edges of eachplate are preferably angularly offset from each other by the same anglethat the side walls 57A, 57B are offset from each other (e.g., 90°).Additionally, the plates 190A, 190B are preferably positioned to receivethe chamber of the vessel between them such that the first side wall 57Ais positioned substantially adjacent and parallel to each of the firstbottom edges 250A, 252A and such that the second side wall 57B ispositioned substantially adjacent and parallel to each of the secondbottom edges 2190B, 252B. This arrangement provides for easy opticalaccess to the optically transmissive side walls 57A, 57B and hence tothe chamber of the vessel. A gel or fluid may optionally be used toestablish or improve optical communication between each optics assemblyand the side walls 57A, 57B. The gel or fluid should have a refractiveindex close to the refractive indexes of the elements that it iscoupling.

[0119] Referring again to FIG. 28, the optics assemblies 216, 218 arepreferably arranged to provide a 90° angle between excitation anddetection paths. The 90° angle between excitation and detection pathsassures that a minimum amount of excitation radiation entering throughthe first side wall of the chamber exits through the second side wall.Also, the 90° angle permits a maximum amount of emitted radiation to becollected through the second side wall. In the preferred embodiment, thevessel 40 includes a locating tab 58 (see FIG. 22) that fits into a slotformed between the optics assemblies 216, 218 to ensure properpositioning of the vessel 40 for optical detection. For improveddetection, the module 147 also preferably includes a light-tight lid(not shown) that is placed over the top of the vessel 40 and madelight-tight to the housing 208 after the vessel is inserted between theplates 190.

[0120] Although it is presently preferred to locate the opticsassemblies 216, 218 next to the bottom edges of the plates 190, manyother arrangements are possible. For example, optical communication maybe established between the optics assemblies 216, 218 and the walls ofthe vessel 40 via optical fibers, light pipes, wave guides, or similardevices. One advantage of these devices is that they eliminate the needto locate the optics assemblies 216, 218 physically adjacent to theplates 190. This leaves more room around the plates in which tocirculate cooling air or refrigerant, so that cooling may be improved.

[0121] The heat-exchanging module 147 also includes a PC board 226 forholding the electronic components of the module and an edge connector224 for connecting the module 147 to the instrument 140 (FIG. 10). Theheating elements and temperature sensors on the plates 190, as well asthe optical boards 220, 222, are connected to the PC board 226 by flexcables (not shown in FIG. 28 for clarity of illustration). The module147 may also include a grounding trace 228 for shielding the opticaldetection circuit. The module 147 may optionally include an indicator,such as an LED 214, for indicating to a user the current status of themodule such as “heating,” “cooling,” “finished,” or “fault”.

[0122] The housing 208 may be molded from a rigid, high-performanceplastic, or other conventional material. The primary functions of thehousing 208 are to provide a frame for holding the plates 190, opticsassemblies 216, 218, fan 212, and PC board 226. The housing 208 alsopreferably provides flow channels and ports for directing cooling airfrom the fan 212 across the surfaces of the plates 190 and out of thehousing. In the preferred embodiment, the housing 208 comprisescomplementary pieces (only one piece shown in the schematic side view ofFIG. 28) that fit together to enclose the components of the module 147between them.

[0123] Referring again to FIG. 23, the plates 190A, 190B may be made ofvarious thermally conductive materials including ceramics or metals.Suitable ceramic materials include aluminum nitride, aluminum oxide,beryllium oxide, and silicon nitride. Other materials from which theplates may be made include, e.g., gallium arsenide, silicon, siliconnitride, silicon dioxide, quartz, glass, diamond, polyacrylics,polyamides, polycarbonates, polyesters, polyimides, vinyl polymers, andhalogenated vinyl polymers, such as polytetrafluoroethylenes. Otherpossible plate materials include chrome/aluminum, superalloys, zircaloy,aluminum, steel, gold, silver, copper, tungsten, molybdenum, tantalum,brass, sapphire, or any of the other numerous ceramic, metal, orpolymeric materials available in the art.

[0124] Ceramic plates are presently preferred because their insidesurfaces may be conveniently machined to very high smoothness for highwear resistance, high chemical resistance, and good thermal contact tothe flexible walls of the reaction vessel. Ceramic plates can also bemade very thin, preferably between about 0.6 and 1.3 mm, for low thermalmass to provide for extremely rapid temperature changes. A plate madefrom ceramic is also both a good thermal conductor and an electricalinsulator, so that the temperature of the plate may be well controlledusing a resistive heating element coupled to the plate.

[0125] Various thermal elements may be employed to heat and/or cool theplates 190A, 190B and thus control the temperature of the reactionmixture in the chamber 42. In general, suitable heating elements forheating the plate include conductive heaters, convection heaters, orradiation heaters. Examples of conductive heaters include resistive orinductive heating elements coupled to the plates, e.g., resistors orthermoelectric devices. Suitable convection heaters include forced airheaters or fluid heat-exchangers for flowing fluids past the plates.Suitable radiation heaters include infrared or microwave heaters.Similarly, various cooling elements may be used to cool the plates. Forexample, various convection cooling elements may be employed such as afan, peltier device, refrigeration device, or jet nozzle for flowingcooling fluids past the surfaces of the plates. Alternatively, variousconductive cooling elements may be used, such as a heat sink, e.g. acooled metal block, in direct contact with the plates.

[0126] Referring to FIG. 24, each plate 190 preferably has a resistiveheating element 206 disposed on its outer surface. The resistive heatingelement 206 is preferably a thick or thin film and may be directlyscreen printed onto each plate 190, particularly plates comprising aceramic material, such as aluminum nitride or aluminum oxide.Screen-printing provides high reliability and low cross-section forefficient transfer of heat into the reaction chamber. Thick or thin filmresistors of varying geometric patterns may be deposited on the outersurfaces of the plates to provide more uniform heating, for example byhaving denser resistors at the extremities and thinner resistors in themiddle. Although it is presently preferred to deposit a heating elementon the outer surface of each plate, a heating element may alternativelybe baked inside of each plate, particularly if the plates are ceramic.The heating element 206 may comprise metals, tungsten, polysilicon, orother materials that heat when a voltage difference is applied acrossthe material. The heating element 206 has two ends which are connectedto respective contacts 204 which are in turn connected to a voltagesource (not shown in FIG. 24) to cause a current to flow through theheating element. Each plate 190 also preferably includes a temperaturesensor 192, such as a thermocouple, thermistor, or RTD, which isconnected by two traces 202 to respective ones of the contacts 204. Thetemperature sensor 192 is be used to monitor the temperature of theplate 190 in a controlled feedback loop.

[0127] The plates have a low thermal mass to enable rapid heating andcooling of the plates. In particular, it is presently preferred thateach of the plates has a thermal mass less than about 5 J/° C., morepreferably less than 3 J/° C., and most preferably less than 1 J/° C. Asused herein, the term thermal mass of a plate is defined as the specificheat of the plate multiplied by the mass of the plate. In addition, eachplate should be large enough to cover a respective major wall of thereaction chamber. In the presently preferred embodiment, for example,each of the plates has a width X in the range of 2 to 22 mm, a length Yin the range of 2 to 22 mm, and a thickness in the range of 0.5 to 5 mm.The width X and length Y of each plate is selected to be slightly largerthan the width and length of the reaction chamber. Moreover, each platepreferably has an angled bottom portion matching the geometry of thebottom portion of the reaction chamber, as previously described withreference to FIG. 34. Also in the preferred embodiment, each of theplates is made of aluminum nitride having a specific heat of about 0.75J/g ° C. The mass of each plate is preferably in the range of 0.005 to5.0 g so that each plate has a thermal mass in the range of 0.00375 to3.75 J/° C.

[0128] The opposing plates 190 are positioned to receive the chamber ofthe vessel 40 between them such that the flexible major walls of thechamber contact and conform to the inner surfaces of the plates. It ispresently preferred that the plates 190 be held in an opposingrelationship to each other using, e.g., brackets, supports, orretainers. Alternatively, the plates 190 may be spring-biased towardseach other as described in International Publication Number WO 98/38487,the disclosure of which is incorporated by reference herein. In anotherembodiment of the invention, one of the plates is held in a fixedposition, and the second plate is spring-biased towards the first plate.If one or more springs are used to bias the plates towards each other,the springs should be sufficiently stiff to ensure that the plates arepressed against the flexible walls of the vessel with sufficient forceto cause the walls to conform to the inner surfaces of the plates.

[0129] FIGS. 29-30 illustrate a preferred support structure 209 forholding the plates 190A, 190B in an opposing relationship to each other.FIG. 29 shows an exploded view of the structure, and FIG. 30 shows anassembled view of the structure. For clarity of illustration, thesupport structure 209 and plates 190A, 190B are shown upside downrelative to their normal orientation in the heat-exchanging module ofFIG. 28. Referring to FIG. 29, the support structure 209 includes amounting plate 210 having the slot 148 formed therein. The slot 148 issufficiently large to enable the chamber of the vessel to be insertedthrough it. Spacing posts 230A, 230B extend from the mounting plate 210on opposite sides of the slot 148. Spacing post 230A has indentations232 formed on opposite sides thereof (only one side visible in theisometric view of FIG. 29), and spacing post 230B has indentations 234formed on opposite sides thereof (only one side visible in the isometricview of FIG. 29). The indentations 232, 234 in the spacing posts are forreceiving the edges of the plates 190A, 190B. To assemble the structure,the plates 190A, 190B are placed against opposite sides of the spacingposts 230A, 230B such that the edges of the plates are positioned in theindentations 232, 234. The edges of the plates are then held in theindentations using a suitable retention means. In the preferredembodiment, the plates are retained by retention clips 236A, 236B.Alternatively, the plates 190A, 190E, may be retained by adhesive bonds,screws, bolts, clamps, or any other suitable means.

[0130] The mounting plate 210 and spacing posts 230A, 230 are preferablyintegrally formed as a single molded piece of plastic. The plasticshould be a high temperature plastic, such as polyetherimide, which willnot deform of melt when the plates 190A, 190B are heated. The retentionclips 230A, 230B are preferably stainless steel. The mounting plate 210may optionally include indentations 240A, 240B for receiving flex cables238A, 238B, respectively, that connect the heating elements andtemperature sensors disposed on the plates 190A, 190B to the PC board226 of the heat-exchanging module 147 (FIG. 28). The portion of the flexcables 238A adjacent the plate 190A is held in the indentation 240A by apiece of tape 242A, and the portion of the flex cables 238B adjacent theplate 190B is held in the indentation 240B by a piece of tape 242B.

[0131]FIG. 31 is an isometric view of the assembled support structure209. The mounting plate 210 preferably includes tabs 246 extending fromopposite sides thereof for securing the structure 209 to the housing ofthe heat-exchanging module. Referring again to FIG. 28, the housing 208preferably includes slots for receiving the tabs to hold the mountingplate 210 securely in place. Alternatively, the mounting plate 210 maybe attached to the housing 208 using, e.g., adhesive bonding, screws,bolts, clamps, or any other conventional means of attachment.

[0132] Referring again to FIG. 29, the support structure 209 preferablyholds the plates 190A, 190B so that their inner surfaces are angled veryslightly towards each other. In the preferred embodiment, each of thespacing posts 230A, 230B has a wall 244 that is slightly tapered so thatwhen the plates 190A, 190B are pressed against opposite sides of thewall, the inner surfaces of the plates are angled slightly towards eachother. As best shown in FIG. 23, the inner surfaces of the plates 190A,190B angle towards each other to form a slightly V-shaped slot intowhich the chamber 42 is inserted. The amount by which the inner surfacesare angled towards each other is very slight, preferably about 1° fromparallel. The surfaces are angled towards each other so that, prior tothe insertion of the chamber 42 between the plates 190A, 190B, thebottoms of the plates are slightly closer to each other than the tops.This slight angling of the inner surfaces enables the chamber 42 of thevessel to be inserted between the plates and withdrawn from the platesmore easily. Alternatively, the inner surfaces of the plates 190A, 190Bcould be held parallel to each other, but insertion and removal of thevessel 40 would be more difficult.

[0133] In addition, the inner surfaces of the plates 190A, 190B arepreferably spaced from each other a distance equal to the thickness ofthe frame 46. In embodiments in which the inner surfaces are angledtowards each other, the centers of the inner surfaces are preferablyspaced a distance equal to the thickness of the frame 46 and the bottomsof the plates are initially spaced a distance that is slightly less thanthe thickness of the frame 46. When the chamber 42 is inserted betweenthe plates 190A, 190B, the rigid frame 46 forces the bottom portions ofthe plates apart so that the chamber 42 is firmly sandwiched between theplates. The distance that the plates 190A, 190B are wedged apart by theframe 46 is usually very small, e.g., about 0.035 mm if the thickness ofthe frame is 1 mm and the inner surfaces are angled towards each otherby 1°.

[0134] Referring again to FIG. 30, the retention clips 236A, 236B shouldbe sufficiently flexible to accommodate this slight outward movement ofthe plates 190A, 190B, yet sufficiently stiff to hold the plates withinthe recesses in the spacing posts 230A, 230B during insertion andremoval of the vessel. The wedging of the vessel between the plates190A, 190B provides an initial preload against the chamber and ensuresthat the flexible major walls of the chamber, when pressurized,establish good thermal contact with the inner surfaces of the plates.

[0135] Referring again to FIG. 28, to limit the amount that the plates190 can spread apart due to the pressurization of the vessel 40, stopsmay be molded into the housings of optics assemblies 216, 218. As shownin FIG. 32, the housing 249 of the optics assembly 218 includesclaw-like stops 247A, 247B that extend outwardly from the housing. Asshown in FIG. 33, the housing 249 is positioned such that the bottomedges of the plates 190A, 190B are inserted between the stops 247A,247B. The stops 247A, 247B thus prevent the plates 190A, 190B fromspreading farther than a predetermined maximum distance from each other.Although not shown in FIG. 33 for illustrative clarity, the opticsassembly 216 (see FIG. 28) has a housing with corresponding stops forpreventing the other halves of the plates from spreading farther thanthe predetermined maximum distance from each other. Referring again toFIG. 23, the maximum distance that stops permit the inner surfaces ofthe plates 190A, 190B to be spaced from each other should closely matchthe thickness of the frame 46. Preferably, the maximum spacing of theinner surfaces of the plates 190A, 190B is slightly larger than thethickness of the frame 46 to accommodate tolerance variations in thevessel 40 and plates 190A, 190B. For example, the maximum spacing ispreferably about 0.1 to 0.3 mm greater than the thickness of the frame46.

[0136]FIG. 35 is a schematic, block diagram of the electronic componentsof the heat-exchanging module 147. The module includes a connector 224or flex cable for connection to the main logic board of the instrument.The module also includes heater plates 190A, 190B each having aresistive heating element as described above. The plates 190A, 190B arewired in parallel to receive power input 253 from the instrument. Theplates 190A, 190B also include temperature sensors 192A, 192B thatoutput analog temperature signals to an analog-to-digital converter 264.The converter 264 converts the analog signals to digital signals androutes them to the microcontroller in the instrument through theconnector 224.

[0137] The heat-exchanging module also includes a cooling system, suchas a fan 212, for cooling the plates 190A, 190B and the reaction mixturecontained in the vessel inserted between the plates. The fan 212 isactivated by switching a power switch 272, which is in turn controlledby a control logic block 270 that receives control signals from themicrocontroller. The module further includes four light sources, such asLEDs 200, for excitation of labeled analytes in the reaction mixture andfour detectors 198, preferably photodiodes, for detecting fluorescentemissions from the reaction mixture. The module also includes anadjustable current source 255 for supplying a variable amount of current(e.g., in the range of 0 to 30 mA) to each LED to vary the brightness ofthe LED. A digital-to-analog converter 260 is connected between theadjustable current source 255 and the microcontroller to permit themicrocontroller to adjust the current source digitally.

[0138] The adjustable current source 255 is preferably used to ensurethat each LED has about the same brightness when activated. Due tomanufacturing variances, many LEDs have different brightnesses whenprovided with the same amount of current. Therefore, it is presentlypreferred to test the brightness of each LED during manufacture of theheat-exchanging module and to store calibration data in a memory 268 ofthe module. The calibration data indicates the correct amount of currentto provide to each LED. The microcontroller reads the calibration datafrom the memory 268 and controls the current source 255 accordingly.

[0139] The module additionally includes a signal conditioning/gainselect/offset adjust block 262 comprised of amplifiers, switches,electronic filters, and a digital-to-analog converter. The block 262adjusts the signals from the detectors 198 to increase gain, offset, andreduce noise. The microcontroller controls block 262 through a digitaloutput register 266. The output register 266 receives data from themicrocontroller and outputs control voltages to the block 262. The block262 outputs the adjusted detector signals to the microcontroller throughthe analog-to-digital converter 264 and the connector 224. The modulealso includes the memory 268, preferably a serial EEPROM, for storingdata specific to the module, such as calibration data for the LEDs 200,thermal plates 190A, 190B, and temperature sensors 192A, 192B.

[0140] The operation of the cartridge and instrument will now bedescribed. As shown in FIG. 3, a fluid sample to be analyzed is added tothe sample chamber 65 through the sample port 64 and the cap 30 screwedinto the port 64 to seal the port shut. Referring to FIG. 10, thecartridge 20 is then placed into the cartridge nest 141 of theinstrument 140 for processing. All valves in the cartridge 20 areinitially closed when the cartridge is placed into the instrument 140.When the cartridge is placed in the instrument, the transducer 92contacts an external surface of the flexible gasket 63 forming thebottom wall of the lysing chamber 86, as shown in FIG. 5.

[0141] Referring again to FIG. 10, the instrument 140 is preferablycomputer-controlled to perform the functions described in the followingsection, e.g., opening and closing valves in the cartridge using valveactuators 142, providing pressure to the cartridge through nozzles 145,activating the transducer 92, sensing liquid presence or liquid levelsusing optical sensors 143 and 144, and controlling the heat-exchangingand optical detection module 147. A programmer having ordinary skill inthe art will be able to program a microcontroller and/or computer toperform these functions based upon the following description.

[0142] Referring to FIG. 9, liquids are preferably forced to flowthrough the cartridge using differential pressure. Although 2o positivepressure is described herein, negative pressure (vacuum) may also beused to control fluid flow in the cartridge. The maximum amount ofpositive pressure that can be applied is usually limited by thehydrophobic membranes which may reach liquid break-through pressureabove 30 psi. The lower limit of pressure is limited by the need to movesample and other fluids through the cartridge sufficiently quickly tomeet assay goals. Below 1 psi, for example, sample may not flowefficiently through the filter stack 87. Pressure in the range of 6 to20 psi is generally adequate. The sample flow rate through the cartridgeis preferably in the range of 10 to 30 ml/minute. The wash flow rate maybe slower, e.g. 6 to 18 ml/minute so that the wash effectively washesthe lysing chamber 86.

[0143] A specific protocol will now be described with reference to FIG.9 to illustrate the operation of the cartridge. It is to be understoodthat this is merely an example of one possible protocol and is notintended to limit the scope of the invention. To begin, the cartridge ispreferably primed with wash solution from the wash chamber 66 before thefluid sample is forced to flow from the sample chamber 65. To prime thecartridge, valves 111 and 115 are opened and a pressure of 10 psi isapplied to the chamber 66 through the pressure port 116 for about twoseconds. A small portion of the wash solution flows through the channels117 and 106, through the lysing chamber 86, through the channels 109 and110, into the U-shaped channel 122, and all the way to the hydrophobicmembrane below the pressure port 128.

[0144] Following priming, valve 115 and pressure port 116 are closed andvalves 107 and 114 are opened. At the same time, a pressure of 20 psi isapplied to the sample chamber 65 through the pressure port 105 for about15 seconds to force the sample to flow through the channel 106, throughthe filter stack 87 in the chamber 87, through the channels 110, 111,112 and into the vented waste chamber 68. As the sample passes thedetection region 136 in the channel 106, the reflective optical sensor144 (FIG. 13) may be used to determine when the sample chamber 65 hasbeen emptied. As the sample liquid flows through the filter stack 87,target cells or viruses in the sample are captured. When a predeterminedvolume of sample reaches the waste chamber 68, some of the liquid spillsover into the sensor chamber 120, triggering the next step in theprotocol. Alternatively, instead of using feedback from optical sensorsto trigger events, the steps in a predetermined protocol may simply betimed, e.g., applying predetermined pressures for predetermineddurations of time to move known volumes of fluid at known flow rates.

[0145] The flow-through design of the lysing chamber 86 permits targetcells or viruses from a relatively large sample volume to beconcentrated into a much smaller volume for amplification and detection.This is important for the detection of low concentration analyte in thesample, such as nucleic acid. In particular, the ratio of the volume ofthe sample forced to flow through the lysing chamber 86 to the volumecapacity of the chamber 86 is preferably at least 2:1, and morepreferably at least 5:1. The volume of sample forced to flow through thechamber 86 is preferably at least 100 μ, and more preferably at least 1ml. In the presently preferred embodiment, a sample volume of 5 ml isforced to flow through the lysing chamber 86, and the chamber 86 has avolume capacity of about 0.5 ml, so that the ratio is 10:1. In addition,the lysing chamber 86 may be sonicated (e.g., using an ultrasonic horncoupled to a wall of the chamber) as the sample is forced to flowthrough the chamber. Sonicating the chamber 86 helps to prevent cloggingof the filter stack 87, providing for more uniform flow through thechamber 86. In particular, the sound waves help keep particulate matteror So the beads in the filter stack from clogging one or more filters.

[0146] In the next step, valves 111, 114, 115 are opened and a pressureof 20 psi is applied to the wash chamber 66 for about seven seconds toforce the wash solution to flow through the channels 117 and 106 intothe lysing chamber 86. The washing solution washes away PCR inhibitorsand contaminants from the lysing chamber 86 and carries then through thechannels 109, 110, and 112 into the waste chamber 68. A variety ofsuitable wash solutions of varying pH, solvent composition, and ionicstrength may be used for this purpose and are well known in the art. Forexample, a suitable washing reagent is a solution of 80 mM potassiumacetate, 8.3 mM Tris-HCl, pH 7.5, 40 uM EDTA, and 55% ethanol. Thelysing chamber 86 may be sonicated (e.g., using an ultrasonic horncoupled to a wall of the chamber) while the wash solution is forced toflow through the chamber. Sonicating the chamber 86 helps to preventclogging of the filter stack 87, providing for more uniform flow throughthe chamber 86 as previously described. In addition, the sound waves mayhelp loosen the material to be washed away. When the incremental volumeof wash solution reaches the waste chamber 68, some of the liquid spillsover into the sensor chamber 121, triggering the next step in theprotocol.

[0147] In the next step, valve 115 is closed and valve 119 is openedwhile a pressure of 15 psi is applied to the reagent chamber 67 throughthe pressure port 118 for about three seconds. The pressure forceslysing reagent to flow from the chamber 67 through the channels 117, 106into the lysing chamber 86, and into the channel 110. The chamber 86 isthus filled with liquid. Suitable lysing reagents include, e.g.,solutions containing a chaotropic salt, such as guanidine HC1, guanidinethiocyanate, guanidine isothiocyanate, sodium iodide, urea, sodiumperchlorate, and potassium bromide. In the presently preferredembodiment, a lysing reagent that is not inhibitory to PCR is used. Thelysing reagent comprises 10 mM tris, 5% tween-20, 1 mM tris(2-carboxyethyl phosphine hydrochloride), 0.1 mM Ethylene Glycol-bis(b-amino-ethyl ether)- N,N,N′, N′-tetracetic acid. After the lysingchamber 86 is filled with lysing reagent, the valves 111, 114 areclosed. Valve 119 remains open and a pressure of 20 psi is applied topressure port 118. The static pressure in the lysis chamber 86 istherefore increased to 20 psi in preparation for the lysis of the cellsor viruses trapped in the filter stack 87.

[0148] Referring again to FIG. 5, the pressurization of the lysingchamber 86 is important because it ensures effective coupling betweenthe transducer 92 and the flexible wall 63 of the lysing chamber 86. Todisrupt the cells or viruses in the chamber 86, the transducer 92 isactivated (i.e., set into vibratory motion). The flexible wall 63 of thelysing chamber 86 transfers the vibratory motion of the transducer 92 tothe liquid in the chamber 86 by allowing slight deflections withoutcreating high stresses in the wall. The wall 63 may be formed by theelastomeric membrane as previously described. Alternatively, the wallmay be a film or sheet of polymeric material (e.g., a polypropylenefilm) preferably having a thickness in the range of 0.025 to 0.1 mm. Thetransducer 92 is preferably an ultrasonic horn for sonicating thechamber 86. The chamber 86 is preferably sonicated for 10 to 40 secondsat a frequency in the range of 20 to 60 kHz. In the exemplary protocol,the chamber is sonicated for 15 seconds at a frequency of 47 kHz. Theamplitude of the horn tip is preferably in the range of 20 to 25 pm(measured peak to peak).

[0149] As the tip of the transducer 92 vibrates, it repeatedly impactsthe flexible wall 63. On its forward stroke (in the upward direction inFIG. 6), the tip of the transducer 92 pushes the wall 63 and creates apressure pulse or pressure wave in the chamber 86. On its retreatingstroke (downward in FIG. 5), the tip of the transducer 92 usuallyseparates from the flexible wall 63 because the flexible wall 63 cannotmove at the same frequency as the transducer. On its next forwardstroke, the tip of the transducer 92 once again impacts the wall 63 in ahead-on collision as the tip and wall speed towards each other. Becausethe transducer 92 and the wall 63 separate as the transducer 92vibrates, the effective forward stroke of the transducer is less thanits peak-to-peak amplitude. The effective forward stroke determines thelevel of sonication in the chamber 86. It is therefore important toincrease the static pressure in the lysing chamber 86 so that when thetip of the transducer 92 retreats, the flexible wall 63 is forcedoutwardly to meet the tip on its return stroke. The static pressure inthe chamber 86 should be sufficient to ensure that the effective forwardstroke of the transducer 92 generates pressure pulses or pressure wavesin the chamber 86. It is presently preferred to increase the staticpressure in the chamber 86 to at least 5 psi above the ambient pressureexternal to the cartridge, and more preferably to a pressure in therange of 15 to 25 psi above the ambient pressure.

[0150] On each forward stroke, the transducer 92 imparts a velocity tothe liquid in the chamber 86, thus creating a pressure wave that quicklysweeps across the chamber 86. The beads in the filter stack 87 (FIG. 6)are agitated by the pressure waves in the chamber 86. The pressure wavespropel the beads into violent motion in the chamber 86, and the beadsmechanically rupture the cells or viruses to release the material (e.g.,nucleic acid) therefrom. It should be noted that some types of cells,such as blood cells, are relatively weak and may be disrupted using onlypressure waves (e.g., ultrasonic waves) without the use of beads. Othertypes of cells (particularly spores) have highly resistant cell wallsand beads are generally required for effective lysis.

[0151] Referring again to FIG. 9, following disruption of the cells orviruses, valves 111, 124 are opened and a pressure of 12 psi isdelivered for about 4 seconds to the reagent chamber 67 through thepressure port 118. The pressure forces the lysis reagent to elute thenucleic acid from the filter stack 87 and to flow with the nucleic acidinto the neutralization chamber 70. The lysing chamber 86 may besonicated (e.g., using an ultrasonic horn coupled to a wall of thechamber) while the eluting the nucleic acid. Sonicating the chamber 86may help prevent clogging of the filter stack 87, as previouslydescribed. The chamber 420 is partially filled (e.g., half-filled) withneutralizer, such as detergent, for neutralizing the lysing reagent. Ifa lysing reagent non-inhibitory to PCR is used, the neutralizer isoptional.

[0152] In the next step, the valve 124 is closed to hold the lysingreagent, analyte, and neutralizer in the chamber 70. The valve 114 isopened and a pressure of 15 psi is applied for about three secondsthrough the pressure port 128 to force any liquid in the U-shapedchannel 122 to flow into the waste chamber 68. Next, valves 124 and 126are opened and a pressure of 15 psi is applied for about five secondsthrough the pressure port 123 on top of the neutralizer chamber 70. Thepressure forces the neutralized lysing reagent and nucleic acid in thechamber 70 to flow into the channel 122 and into the master mix chamber71. The valve 126 to the master mix chamber 71 is then closed. Themaster mix chamber contains PCR reagents and fluorescent probes that mixwith the neutralized lysing reagent and nucleic acid to form a reactionmixture.

[0153] In the next step, the channel 122 is cleared by opening valve 114to waste chamber 68 and applying a pressure of 15 psi for about onesecond to pressure port 128. In the next step, the reaction mixtureformed in the master mix chamber 71 is moved into the reaction vessel 40as follows. Valves 126, 127, and 133 are opened and a pressure of 15 psiis applied for about six seconds to the pressure port 125 on top of themaster mix chamber 71 to force the reaction mixture to flow through thechannel 122, valve 127, and channel 80 into the reaction vessel 40through the port 41. The reaction mixture fills the chamber 42 of thevessel, displacing air in the chamber which exits through the outletchannel 52. The air escaping through the outlet channel 52 travels inchannel 81 past sensor region 130 and into channel 131. From channel131, the air flows into channel 132, through valve 133, channel 134, andexits the cartridge through the vent 36. When a volume of reactionmixture sufficient to fill the chamber 42 has flowed into the vessel,excess reaction mixture exits the vessel through the outlet channel 52.The excess reaction mixture flows into channel 81 and is opticallydetected in the sensor region 130. When the reaction mixture isdetected, valve 133 is closed while pressure from the pressure port 125is applied to pressurize the reaction chamber 42.

[0154] Referring again to FIG. 23, the pressurization of the chamber 42expands the flexible major walls 48 of the vessel. In particular thepressure forces the major walls 48 to contact and conform to the innersurfaces of the plates 190A, 190B. This ensures optimal thermalconductance between the plates 190A, 190B and the reaction mixture inthe chamber 42. It is presently preferred to pressurize the chamber 42to a pressure in the range of 2 to 30 psi above ambient pressure. Thisrange is presently preferred because 2 psi is generally enough pressureto ensure conformity between the walls 48 and the surfaces of the plates190A, 190B, while pressures above 30 psi may cause bursting of the walls48, deformation of the frame 46 or plates 190A, 190B, or bursting of thehydrophobic membranes in the cartridge. More preferably, the chamber 42is pressurized to a pressure in the range of 8 to 15 psi above ambientpressure. This range is more preferred because it is safely within thepractical limits described above. When the chamber 42 is pressurized,the reaction mixture in the vessel 40 is thermally processed andoptically interrogated to determine the presence or absence of a targetanalyte in the mixture.

[0155] Referring again to FIG. 35, the reaction mixture is thermallyprocessed between the plates 190A, 190B using standardproportional-integral-derivative (PID) control using target temperaturesand feedback signals from the temperature sensors 192A, 192B.Proportioning may be accomplished either by varying the ratio of “on”time to “off” time, or, preferably with proportional analog outputswhich decrease the average power being supplied either to the heatingelements on the plates 190A, 190B or to the fan 212 as the actualtemperature of the plates 190A, 190B approaches the desired set pointtemperature. PID control combines the proportional mode with anautomatic reset function (integrating the deviation signal with respectto time) and rate action (summing the integral and deviation signal toshift the proportional band). Standard PID control is well known in theart and need not be described further herein. Alternatively, thereaction mixture may be thermally processed using a modified version ofPID control described in International Publication Number WO 99/48608(Application Number PCT/US99/06628) the disclosure of which isincorporated by reference herein.

[0156] As the reaction mixture is thermally cycled between the heaterplates 190A, 190B to amplify one or more target nucleic acid sequencesin the mixture, the mixture is optically interrogated, preferably at thelowest temperature point in each cycle. Optical interrogation isaccomplished by sequentially activating each of the LEDs 200 to excitedifferent fluorescently-labeled analytes in the mixture and by detectinglight emitted (fluorescent output) from the chamber 42 using detectorsthe 198. Referring again to FIG. 22, excitation beams are preferablytransmitted to the chamber 42 through the optically transmissive sidewall 57A, while fluorescent emission is detected through the side wall57B.

[0157] One advantage of the cartridge of the present invention is thatit allows the intracellular material from a relatively large volume offluid sample, e.g. several milliliters or more, to be separated from thesample and concentrated into a much smaller volume of reaction fluid,e.g., 100 μL or less. The cartridge permits extraordinary concentrationfactors by efficiently extracting material from milliliter quantities offluid sample. In particular, the sample chamber 65 preferably has avolume capacity in the range of 100 μl to 12 ml. More preferably, thesample chamber 65 has a volume capacity of at least 1 ml. The lowerlimit of 1 ml is preferred because at least 1 ml of sample should beanalyzed to detect low concentration analytes such as nucleic acid. Theupper limit of 12 ml is preferred because a sample volume greater than12 ml would require a much larger cartridge and likely clog the filterstack. In the presently preferred embodiment, the sample chamber has avolume capacity of 5.5 ml for holding 5 ml of sample.

[0158] The wash chamber 66 has a volume capacity proportional to thevolume of the lysing chamber 86. In particular, the wash chamber 66preferably holds a volume of wash that is at least one to two times thevolume of the lysing chamber 86 to ensure that there is enough washsolution to wash out PCR inhibitors and debris from the chamber 86. Inthe presently preferred embodiment, the volume of the lysing chamber 86is about 0.5 ml and the volume of the wash chamber 66 is 2.5 ml forholding 2 ml of wash solution. The lysing chamber volume of 0.5 ml is acompromise between a size large enough to avoid clogging of the filterstack 87 and a size small enough to concentrate analyte into a smallvolume for improved amplification and detection.

[0159] The reagent chamber 67 preferably holds a volume of lysingreagent that is at least one to two times the volume of the lysingchamber 86 so that there is sufficient lysing reagent to pressurize thechamber and to elute nucleic acid from the chamber. In the presentlypreferred embodiment, the chamber 67 has a volume capacity of 1.5 ml forholding about 1 to 1.5 ml of lysing reagent. The waste chamber 68 has avolume capacity sufficient to hold the sample, wash solution, and unusedlysing reagent. The waste chamber 68 is sized at 9.5 ml volume capacityin the preferred embodiment.

[0160] The size of the neutralization chamber 70 is dependent upon thevolume of the lysing chamber 86 since the neutralizer in the chamber 70neutralizes the volume of lysing reagent that fills lo the lysingchamber 86. It is currently preferred that the lysing chamber have avolume if 0.5 ml, so the chamber 70 has a volume capacity of 1.0 ml forholding about 0.5 ml of neutralizer that is mixed with 0.5 ml of thelysing reagent and eluted analyte. The volume capacity of the master mixchamber 71 should be sufficient to produce a reaction mixture to fillthe vessel 40 and the channels 122, 127 leading to the vessel. In thepresently preferred embodiment, the master mix chamber has a volumecapacity of 200 pl for holding an initial load of 100 μl of master mixto which is added 100 μl of neutralized lysing reagent and elutedanalyte to form the reaction mixture.

[0161] The flow channels in the cartridge are generally D-shaped incross section (with the gasket 63 forming the flat side of the channel)and preferably have a width or diameter in the range of {fraction(1/64)} to ⅛ of an inch (0.4 to 3.2 mm), and more preferably a width of{fraction (1/32)} to {fraction (1/16)} of an inch (0.8 to 1.6 mm). Theseranges are presently preferred to avoid having channels to narrow (whichcreates flow restriction) and to avoid having channels too wide (whichyields unused volumes of liquid sitting in the flow path).

[0162] Many modifications to the structure and operation of thecartridge and instrument are possible in alternative embodiments. Forexample, although amplification by PCR is presently preferred, thecartridge and instrument may be used to amplify nucleic acid sequencesusing any amplification method, including both thermal cyclingamplification methods and isothermal amplification methods. Suitablethermal cycling methods include, but are not limited to, the PolymeraseChain Reaction (PCR; U.S Pat. Nos. 4,683,202, 4,683,195 and 4,965,188);Reverse Transcriptase PCR (RT-PCR); DNA Ligase Chain Reaction (LCR;International Patent Application No. WO 89/09835); andtranscription-based amplification (D. Y. Kwoh et al. 1989, Proc. Natl.Acad. Sci. USA 86, 1173-1177). Suitable isothermal amplification methodsuseful in the practice of the present invention include, but are notlimited to, Rolling Circle Amplification; Strand DisplacementAmplification (SDA; Walker et al. 1992, Proc. Nati. Acad. Sci. USA 89,392-396); Q-.beta. replicase (Lizardi et al. 1988, Bio/Technology 6,1197-1202); Nucleic Acid-Based Sequence Amplification (NASBA; R.Sooknanan and L. Malek 1995, Bio/Technology 13, 563-65); andSelf-Sustained Sequence Replication (3SR; Guatelli et al. 1990, Proc.Nati. Acad. Sci. USA 87, 1874-1878).

[0163] Moreover, the cartridge and instrument may be used to conductchemical reactions other than nucleic acid amplification. Further,although fluorescence excitation and emission detection is preferred,optical detection methods such as those used in direct absorption and/ortransmission with on-axis geometries may also be used to detect analytein the cartridge. Another possible detection method is time decayfluorescence. Additionally, the cartridge is not limited to detectionbased upon fluorescent labels. For example, detection may be based uponphosphorescent labels, chemiluminescent labels, orelectrochemiluminescent labels.

[0164] A fluid sample may be introduced into the cartridge by a varietyof means, manual or automated. For manual addition, a measured volume ofmaterial may be placed into a receiving area of the cartridge through aninput port and a cap is then placed over the port. Alternatively, agreater amount of sample material than required for the analysis can beadded to the cartridge and mechanisms within the cartridge can effectthe precise measuring and aliquoting of the sample needed for thespecified protocol. It may be desirable to place certain samples, suchas tissue biopsy material, soil, feces, exudates, and other complex lomaterial into another device or accessory and then place the secondarydevice or accessory into the cartridge. For example, a piece of tissuemay be placed into the lumen of a secondary device that serves as thecap to the input port of the cartridge. When the cap is pressed into theport, the tissue is forced through a mesh that slices or otherwisedivides the tissue.

[0165] For automated sample introduction, additional design features ofthe cartridge are employed and, in many cases, impart specimen accessionfunctionality directly into the cartridge. With certain samples, such asthose presenting a risk of hazard to the operator or the environment,such as human retrovirus pathogens, the transfer of the sample to thecartridge may pose a risk. Thus, in one embodiment, a syringe may beintegrated into a device to provide a means for moving external fluidicsamples directly into the cartridge. Alternatively, a venous punctureneedle and an evacuated blood tube can be attached to the cartridgeforming an assembly that can be used to acquire a sample of blood. Aftercollection, the tube and needle are removed and discarded, and thecartridge is then placed in an instrument to effect processing. Theadvantage of such an approach is that the operator or the environment isnot exposed to pathogens.

[0166] The input port can be designed with a consideration ofappropriate human factors as a function of the nature of the intendedspecimen. For example, respiratory specimens may be acquired from thelower respiratory tract as expectorants from coughing, or as swab orbrush samples from the back of the throat or the nares. In the formercase, the input port can be designed to allow the patient to coughdirectly into the cartridge or to otherwise facilitate spitting of theexpectorated sample into the cartridge. For brush or swab specimens, thespecimen is placed into the input port where features of the port andclosure facilitate the breaking off and retaining of the end of the swabor brush in the cartridge receiving area.

[0167] In another embodiment, the cartridge includes input and outputtubes that may be positioned in a sample pool of very large volume, suchas a flowing stream of water, so that the sample material flows throughthe cartridge. Alternatively, a hydrophilic wicking material can serveas an interactive region so that the entire cartridge can be immerseddirectly into the specimen, and a sufficient amount of specimen isabsorbed into the wicking material. The cartridge is then removed, andcan be transported to the laboratory or analyzed directly using aportable instrument. In another embodiment, tubing can be utilized sothat one end of the tube is in direct communication with the cartridgeto provide a fluidic interface with at least one interactive region andthe other end is accessible to the external environment to serve as areceiver for sample. The tube can then be placed into a specimen andserve as a sipper. The cartridge itself may also serve as the actualspecimen collection device, thereby reducing handling and inconvenience.In the case of specimens involved in legal disputes or criminalinvestigations, the direct accessing of the test material into thefluidic cartridge is advantageous because the chain of custody isconveniently and reliably preserved.

[0168] Referring again to FIG. 9, reagents may be exogenously introducedinto the cartridge before use, e.g., through sealable openings in thereagent chamber 67, neutralizer chamber 70, and master mix chamber 71.Alternatively, the reagents may be placed in the cartridge duringmanufacture, e.g., as aqueous solutions or dried reagents requiringreconstitution. The particular format is selected based on a variety ofparameters, including whether the interaction is solution-phase orsolid-phase, the inherent thermal stability of the reagent, speed ofreconstitution, and reaction kinetics. Reagents containing compoundsthat are thermally unstable when in solution can be stabilized by dryingusing techniques such as lyophilization. Additives, such as simplealcohol sugars, methylcelluloses, and bulking proteins may be added tothe reagent before drying to increase stability or reconstitutability.

[0169] Referring again to FIG. 21, the reaction vessel 40 does notrequire two flexible sheets forming opposing major walls 48 of thereaction chamber 42. For example, in one alternative embodiment, thevessel 40 has only one flexible sheet forming a major wall of thechamber. The rigid frame 46 defines the other major wall of the chamber,as well as the side walls of the chamber. In this embodiment, the majorwall formed by the frame 46 should have a minimum thickness of about0.05 inches (1.25 mm) which is typically the practical minimum thicknessfor injection molding, while the flexible sheet may be as thin as 0.0005inches (0.0125 mm). The advantage to this embodiment is that themanufacturing of the reaction vessel 40 is simplified, and hence lessexpensive, since only one flexible sheet need be attached to the frame46. The disadvantage is that the heating and cooling rates of thereaction mixture are likely to be slower since the major wall formed bythe frame 46 will probably not permit as high a rate of heat transfer asthe thin, flexible sheet.

[0170] Referring to FIG. 28, the heat-exchanging module 147 onlyrequires one thermal surface for contacting a flexible wall of thereaction vessel 40 and one thermal element for heating and/or coolingthe thermal surface. The advantage to using one thermal surface and onethermal element is that the apparatus may be manufactured lessexpensively. The disadvantage is that the heating and cooling rates arelikely to be about twice as slow. Further, although it is presentlypreferred that the thermal surfaces be formed by the thermallyconductive plates 190, each thermal surface may be provided by any rigidstructure having a contact area for contacting a wall of the vessel 40.The thermal surface preferably comprises a material having a highthermal conductivity, such as ceramic or metal. Moreover, the thermalsurface may comprise the surface of the thermal element itself. Forexample, the thermal surface may be the surface of a thermoelectricdevice that contacts the wall to heat and/or cool so the chamber.

[0171] It is presently preferred to build the transducer into theinstrument 140. In another embodiment, however, the transducer may bebuilt into the cartridge. For example, a piezoelectric disk may be builtinto the cartridge for sonicating the lysing chamber. Alternatively, aspeaker or electromagnetic coil device may be built into the cartridge.In these embodiments, the cartridge includes suitable electricalconnectors for connecting the transducer to a power supply. Inembodiments in which the transducer is built into the cartridge, thetransducer should be prevented from contacting the fluid sampledirectly, e.g., the transducer should be laminated or separated from thesample by a chamber wall. Further, lysis of the cells or viruses may beperformed using a heater in place of or in combination with atransducer. The heater may be a resistive heating element that is partof cartridge, or the heater could be built into the instrument thatreceives the cartridge. In this embodiment, the cells or viruses aredisrupted by heating the lysis chamber to a high temperature (e.g., 95°C.) to disrupt the cell walls.

[0172] FIGS. 36-46 show another apparatus 350 for disrupting cells orviruses according to the present invention. FIG. 36 shows an isometricview of the apparatus 350, and FIG. 37 shows a cross sectional view ofthe apparatus 350. As shown in FIGS. 36-37, the apparatus 350 includes acartridge or container 358 having a chamber 367 for holding the cells orviruses. The container includes a flexible wall 440 defining the chamber367. In this embodiment, the flexible wall 440 is the bottom wall of thechamber 367. The flexible wall 440 is preferably a sheet or film ofpolymeric material (e.g., a polypropylene film) and the wall 440preferably has a thickness in the range of 0.025 to 0.1 mm. Theapparatus 350 also includes a transducer 314, such as an ultrasonichorn, for contacting an external surface of the flexible wall 440 (i.e.,a surface of the wall 440 that is external to the chamber 367). Thetransducer 314 should be capable of vibratory motion sufficient tocreate pressure pulses in the chamber 367. Suitable transducers includeultrasonic, piezoelectric, magnetostrictive, or electrostatictransducers. The transducer may also be an electromagnetic device havinga wound coil, such as a voice coil motor or a solenoid device.

[0173] The apparatus 350 further includes a support structure 352 forholding the container 358 and the transducer 314 against each other suchthat the transducer 314 contacts the wall 440 of the chamber 367 and forapplying a substantially constant force to the container 358 or to thetransducer 314 to press together the transducer 314 and the wall 440 ofthe chamber. The support structure 352 includes a base structure 354having a stand 356. The transducer 314 is slidably mounted to the basestructure 354 by a guide 364. The guide 364 is either integrally formedwith the base structure 354 or fixedly attached to the base structure.The support structure 352 also includes a holder 360 attached to thebase structure 354 for holding the container 358. The holder 360 has aU-shaped bottom portion providing access to the flexible wall 440 of thechamber 367. The guide 364 and the holder 360 are arranged to hold thetransducer 314 and the container 358, respectively, such that theexternal surface of the wall 440 contacts the transducer 314. Thesupport structure 352 also includes a top retainer 362 for the container358. The retainer 362 is U-shaped to allow access to an exit port 444formed in the container 358.

[0174] The support structure 352 further includes an elastic body, suchas a spring 366, for applying a force to the transducer 314 to press thetransducer 314 against the wall 440. When the transducer 314 is incontact with the wall 440, the force provided by the spring 366 isconstant, providing for consistent coupling between the transducer 314and the wall 440. The spring 366 is positioned between a spring guide372 and the base of a coupler 368 that supports the bottom of thetransducer 314. As shown in FIG. 36, the coupler 370 preferably has awindow 370 through which the power cord (not shown) of the transducer314 may be placed. Bolts or screws 376 hold the spring guide 372 inadjustment grooves 374 formed in the base structure 354. The magnitudeof the force provided by the spring 366 may be adjusted by changing thepreload on the spring. To adjust the preload on the spring 366, thebolts 376 holding the spring guide 372 are loosened, the guide 372 ismoved to a new position, and the bolts 376 are retightened to hold theguide 372 in the new position.

[0175] Once the preload on the spring 366 is adjusted to provide asuitable coupling force between the transducer 314 and the wall 440, itis desirable to keep the preload constant from one use of the apparatus350 to the next so that valid comparisons can be made between differentsamples disrupted by the apparatus.

[0176] The magnitude of the force provided by the spring 366 to presstogether the transducer 314 and the wall 440 is important for achievinga consistent transfer of energy between the transducer 314 and thechamber 367. If the force is too light, the transducer 314 will only beheld lightly against the wall 440, leading to poor translation ofvibratory movement from the transducer 314 to the wall 440. If the forceis too strong, the container 358 or wall 440 may be damaged duringsonication. An intermediate force results in the most consistent andrepeatable transfer of vibratory motion from the transducer 314 to thewall 440. It is presently preferred that the spring 366 provide a forcein the range of 1 to 5 lbs., with a force of about 2 lbs. being the mostpreferred.

[0177]FIG. 38 shows an exploded view of the container 358, and FIG. 39shows an assembled view of the container 358. As shown in FIGS. 38-39,the container 358 has a body comprising a top piece 448, a middle piece450, and a bottom piece 452. The middle piece 450 defines an inlet port442 to the chamber 367, and the top piece 448 defines an outlet port 444to the chamber. The ports 442, 444 are positioned to permit thecontinuous flow of a fluid sample through the chamber 367. The flexiblewall 440 is held between the middle and bottom pieces 450, 452 usinggaskets 453, 454. Alternatively, the flexible wall 440 may simply beheat sealed to the middle piece 450 so that the bottom piece 452 andgaskets 453, 454 may be eliminated.

[0178] The container 358 also includes a filter stack 446 in the chamber367 for capturing sample components (e.g., target cells or viruses) asthe sample flows through the chamber 367. The filter stack comprises(from bottom to top in FIGS. 38-39) a gasket 456, a first filter 458, agasket 460, a second filter 464 having a smaller average pore size thanthe first filter 458, and a gasket 466. The filter stack is held betweenthe top and middle pieces 448, 450 of the container 358. The filterstack also includes beads 462 disposed between the first and secondfilters 458 and 464. The gasket 460 spaces the first filter 458 from thesecond filter 464. The gasket 460 should be thick enough to permit thebeads to move freely in the space between the filters 458, 464. A fluidsample flowing through the chamber 367 first flows through the filter458 and then through the filter 466. After flowing through the filterstack, the sample flows along flow ribs 468 (FIG. 38) formed in theportion of the top piece 448 that defines the top of the chamber andthrough the outlet port 444 (FIG. 39).

[0179] The filter stack is effective for capturing cells or viruses as afluid sample flows through the chamber 367 without clogging of the. Thefirst filter 458 (having the largest pore size) filters out coarsematerial such as salt crystals, cellular debris, hair, tissue, etc. Thesecond filter 464 (having a smaller pore size) captures target cells orviruses in the fluid sample. The average pore size of the first filter458 is selected to be small enough to filter coarse material from thefluid sample (e.g., salt crystals, cellular debris, hair, tissue) yetlarge enough to allow the passage of the target cells or viruses. Ingeneral, the average pore size of the first filter 458 should be in therange of about 2 to 25 μm, with a presently preferred pore size of about5 μm. The average pore size of the second filter 464 is selected to beslightly smaller than the average size of the target cells or viruses tobe captured (typically in the range of 0.2 to 5 μm).

[0180] The beads 462 are useful for disrupting the captured cells orviruses to release the intracellular material (e.g., nucleic acid)therefrom. Movement of the beads 462 ruptures the cells or virusescaptured on the filter 464. Suitable beads for rupturing cells orviruses include borosilicate glass, lime glass, silica, and polystyrenebeads. The beads may be porous or non-porous and preferably have anaverage diameter in the range of 1 to 200 pm. In the presently preferredembodiment, the beads 462 are polystyrene beads having an averagediameter of about 100 μm.

[0181] The beads 462 may have a binding affinity for target cells orviruses in the fluid sample to facilitate capture of the target cells orviruses. For example, antibodies or certain receptors may be coated ontothe surface of the beads 462 to bind target cells in the sample.Moreover, the chamber 367 may contain two different types of beads forinteracting with target cells or viruses. For example, the chamber maycontain a first set of beads coated with antibodies or receptors forbinding target cells or viruses and a second set of beads (intermixedwith the first set) for rupturing the captured cells or viruses. Thebeads in the chamber may also have a binding affinity for theintracellular material (e.g., nucleic acid) released from the rupturedcells or viruses. Such beads may be useful for isolating target nucleicacid for subsequent elution and analysis. For example, the chamber 367may contain silica beads to isolate DNA or cellulose beads with oligo dTto isolate messenger RNA for RT-PCR. The chamber 367 may also containbeads for removing unwanted material (e.g., proteins, peptides) orchemicals (e.g., salts, metal ions, or detergents) from the sample thatmight inhibit PCR.

[0182] To ensure that the air bubbles can escape from the chamber 367,it is desirable to use the container 358 in an orientation in whichliquid flows up (relative to gravity) through the filters 458, 464 andthe chamber 367. The upward flow through the chamber 5 367 aids the flowof air bubbles out of the chamber. Thus, the inlet port 442 for entry offluids into the chamber 367 should generally be at a lower elevationthan the outlet port 444. The volume capacity of the chamber 367 isusually in the range of 50 to 500 μl. The volume capacity of the chamber367 is selected to provide for concentration of analyte separated from afluid sample without the chamber being so small that the filters 458,464 become clogged.

[0183] The pieces 448, 450, 452 forming the body of the container 358are preferably molded polymeric parts (e.g., polypropylene,polycarbonate, acrylic, etc.). Although molding is preferred for massproduction, it also possible to machine the top, middle, and bottompieces 448, 450, 452. The pieces 448, 450, 452 may be held together byscrews or fasteners. Alternatively, ultrasonic to bonding, solventbonding, or snap fit designs could be used to assemble the container358. Another method for fabricating the container 358 is to mold thebody as a single piece and heat seal the flexible wall 440 and thefilters 458, 464 to the body.

[0184]FIG. 40 shows a fluidic system for use with the apparatus. Thesystem includes a bottle 470 for holding lysis buffer, a bottle 472containing wash solution, and a sample container 474 for holding a fluidsample. The bottles 470, 472 and sample container 474 are connected viatubing to the valve ports of a syringe pump 476. The inlet port of thecontainer 358 is also connected to the syringe pump 476. The outlet portof the container 358 is connected to the common port of a distributionvalve 478. The system also includes a collection tube 480 for receivingintracellular material removed from the sample, a waste container 482for receiving waste, and a pressure source, such as a pump 484. Thecollection tube 480, waste container 482, and pump 484 are connected torespective peripheral ports of the distribution valve 478. A pressureregulator 486 regulates the pressure supplied by the pump 484.

[0185] A specific protocol will now be described with reference to FIGS.39-40 to illustrate the operation of the container 358. It is to beunderstood that this is merely an example of one possible protocol andis not intended to limit the scope of the invention. The syringe pump476 pumps a fluid sample from the sample container 474 through thecontainer 358 and into the waste container 482. As the fluid sample isforced to flow through the filters in the chamber 367, coarse materialis filtered by the filter 458 and target cells or viruses in the sampleare captured by the filter 464. The chamber 367 may be sonicated as thesample is forced to flow through the chamber to help prevent clogging ofthe filters. Next, the syringe pump 476 pumps wash solution from thebottle 472 through the container 358 and into the waste container 482.The washing solution washes away PCR inhibitors and contaminants fromthe chamber 367.

[0186] In the next step, the syringe pump 476 pumps lysis buffer fromthe bottle 470 into the container 358 so that the chamber 367 is filledwith liquid. The lysis buffer should be a medium through which pressurewaves can be transmitted. For example, the lysis buffer may comprisedeionized water for holding the cells or viruses in suspension orsolution. Alternatively, the lysis buffer may include one or more lysingagents to aid in the disruption of the cells or viruses. One of theadvantages of the present invention, however, is that harsh lysingagents are not required for successful disruption of the cells orviruses. Next, the distribution valve of the syringe pump 476 is closedupstream of the container 358, and the distribution valve 478 is opened.The pump 484 then pressurized the chamber 367 through the outlet port444, preferably to about 20 psi above the ambient pressure. Thedistribution valve 478 downstream of the container 358 is then closed.The static pressure in the chamber 367 is therefore increased to about20 psi in preparation for the disruption of the cells or viruses trappedon the filter 464.

[0187] Referring again to FIG. 37, the pressurization of the chamber 367is important because it ensures effective coupling between thetransducer 314 and the flexible wall 440. To disrupt the cells orviruses in the chamber 367, the transducer 314 is activated (i.e., setinto vibratory motion). The flexible wall 440 transfers the vibrationalmotion of the transducer 314 to the liquid in the chamber 367 byallowing slight deflections without creating high stresses in the wall.The transducer 314 is preferably an ultrasonic horn for sonicating thechamber 367. The chamber 367 is preferably sonicated for 10 to 40seconds at a frequency in the range of 20 to 60 kHz. In the exemplaryprotocol, the chamber is sonicated for 15 seconds at a frequency of 40kHz. The amplitude of the horn tip is preferably in the range of 20 to25 μm (measured peak to peak).

[0188] As the tip of the transducer 314 vibrates, it repeatedly impactsthe flexible wall 440. On its forward stroke (in the upward direction inFIG. 37), the tip of the transducer 314 pushes the wall 440 and createsa pressure pulse or pressure wave in the chamber 367. On its retreatingstroke (downward in FIG. 37), the tip of the transducer 314 usuallyseparates from the flexible wall 440 because the flexible wall 440cannot move at the same frequency as the transducer. On its next forwardstroke, the tip of the transducer 314 once again impacts the wall 440 ina head-on collision as the tip and wall speed towards each other.

[0189] Because the transducer 314 and the wall 440 separate as thetransducer 314 vibrates, the effective forward stroke of the transduceris less than its peak-to-peak amplitude. The effective forward strokedetermines the level of sonication in the chamber 367. It is thereforeimportant to increase the static pressure in the chamber 367 so thatwhen the tip of the transducer 314 retreats, the flexible wall 440 isforced outwardly to meet the tip on its return stroke. The staticpressure in the chamber 367 should be sufficient to ensure that theeffective forward stroke of the transducer 314 generates the necessarypressure pulses or pressure waves in the chamber to effect celldisruption. It is presently preferred to increase the static pressure inthe chamber 367 to at least 5 psi above the ambient pressure, and morepreferably to a pressure in the range of 15 to 25 psi above the ambientpressure.

[0190] On each forward stroke, the transducer 314 imparts a velocity tothe liquid in the chamber 367, thus creating a pressure wave thatquickly sweeps across the chamber. The beads 462 in the filter stack 446(FIG. 38) are agitated by the pressure waves in the chamber 367. Thepressure waves propel the beads into violent motion, and the beadsmechanically rupture the cells or viruses to release the analyte (e.g.,nucleic acid) therefrom. Referring again to FIG. 40, followingdisruption of the cells or viruses, the syringe pump 476 pumps thereleased intracellular material from the container 358 into thecollection tube 480.

[0191]FIG. 41 shows another embodiment of the invention in which thecontainer 358 has a solid wall 488 for contacting the transducer 314.The solid wall 488 differs from the flexible wall 440 previouslydescribed with reference to FIG. 37. Whereas the flexible wall istypically a thin film that bends under its own weight and does not holdits shape unless held on its edges, the solid wall 488 holds it shapewhen unsupported. The advantage of using a solid wall to contact thetransducer 314 is that there is no need to pressurize the chamber 367 toensure effective coupling between the wall 488 and the transducer 314.The elastic restoring force of the solid wall 488 provides the necessarycoupling between the wall and the transducer 314. However, the properdesign of the solid wall 488 is necessary so that the wall is notdamaged (e.g., melted) by the vibratory movements of the transducer 314.

[0192] In particular, the solid wall 488 should have a natural frequencythat is higher than the vibrating frequency at which the transducer 314is operated. Preferably, the ratio of the natural frequency of the wall488 to the vibrating frequency is at least 2:1, and more preferably theratio is at least 4:1. In addition, the wall 488 should not be so rigidthat it cannot transfer the vibratory motion of the transducer to theliquid in the chamber 367. It is preferred that the wall 488 be capableof deflecting a distance in the range of 5 to 40 μm, and more preferablyabout 20 μm peak to peak when the transducer 314 applies a force in therange of 1 to 10 lbs. to the external surface of the wall 488. It ismore preferable that the wall 488 be capable of deflecting a distance inthe range of 5 to 40 μm, and more preferably about 20 μm peak to peakwhen the transducer 314 applies a force in the range of 2 to 5 lbs. Toachieve these criteria, the wall 488 is dome-shaped and convex withrespect to the transducer 314(i.e., the wall 488 curves outwardlytowards the transducer). The advantage to the dome-shaped design of thewall 488 is that the dome shape increases the natural frequency of thewall (compared to a flat wall) without causing the wall to be so stiffthat it cannot transfer the vibratory movements of the transducer 314 tothe chamber 367.

[0193]FIG. 42 shows a cross sectional view of the wall 488. Thedome-shaped portion 495 of the wall preferably has a radius of curvatureR in the range of 6.3 to 12.7 mm when the diameter D of the dome-shapedportion is about 11.1 mm. More preferably, the dome-shaped portion 495of the wall preferably has a radius of curvature R of about 9.5 mm whenthe diameter D of the dome-shaped portion is about 11.1 mm. The wall 488also includes a flat outer rim 497 for clamping the wall 488 in thecontainer 358. Alternatively, the wall 488 may be integrally molded witheither of pieces 450, 452 (FIG. 41). The thickness T of the wall ispreferably in the range of 0.25 to 1 mm. If it is less than 0.25 mmthick, the wall 488 may be too weak. If the wall has a thickness greaterthan 1 mm, the wall may be too stiff to deflect properly in response tothe vibratory movements of the transducer. In the presently preferredembodiment, the wall 488 has a thickness T of about 0.5 mm. The wall 488is preferably a molded plastic part. Suitable materials for the wall 488include Delrin® (acetal resins or polymethylene oxide), polypropylene,or polycarbonate.

[0194] The interaction of the transducer 314 with the solid wall 488will now be described with reference to FIG. 41. Prior to activating thetransducer, target cells or viruses are captured on the filter 490 byforcing a fluid sample to flow though the chamber 367 (e.g., using thefluidic system previously described with reference to FIG. 40). Inaddition, the chamber 367 is filled with a liquid (e.g., lysis buffer)as previously described. Unlike the previously described embodiments,however, the chamber 367 does not require pressurization. Instead, it ispreferred that ambient pressure is maintained in the chamber. Thetransducer 314 is placed in contact with the external surface of thewall 488, preferably using a support structure as previously describedwith reference to FIG. 37. In particular, a spring preferably pushes thetransducer against the wall 488 with a force in the range of 1 to 10lbs., and more preferably in the range of 2 to 5 lbs.

[0195] To disrupt the cells or viruses in the chamber 367, thetransducer 314 is activated (i.e., induced into vibratory motion). Asthe tip of the transducer 314 vibrates, it deflects the wall 488. On itsforward stroke (in the upward direction in FIG. 41), the tip of thetransducer 314 pushes the wall 488 and creates a pressure pulse orpressure wave in the chamber 367. On its retreating stroke (downward inFIG. 41), the wall 488 remains in contact with the tip of the transducer314 because the wall 488 has a natural frequency higher than thevibrating frequency of the transducer. In embodiments in which thetransducer is an ultrasonic horn for sonicating the chamber 367, thechamber 367 is preferably sonicated for 10 to 40 seconds at a frequencyin the range of 20 to 40 kHz. In the exemplary protocol, the chamber issonicated for 15 seconds at a frequency of 40 kHz. The amplitude of thehorn tip is preferably in the range of 20 to 25 μm (measured peak topeak), and the natural frequency of the wall 488 should be greater than40 kHz, preferably at least 80 kHz, and more preferably at least 160kHz.

[0196] One advantage to using the solid interface wall 488 is thatstrong pressure drops can be achieved in the chamber 367 as long as thestatic pressure in the chamber is low. For example, at atmosphericpressure, cavitation (the making and breaking of microscopic bubbles)can occur in the chamber 367. As these bubbles or cavities grow toresonant size, they collapse violently, producing very high localpressure changes. The pressure changes provide a mechanical shock to thecells or viruses, resulting in their disruption. The disruption of thecells or viruses may also be caused by sharp pressure rises resultingfrom the vibratory movement of the transducer 314. In addition, thedisruption of the cells or viruses may be caused by the violent motionof the beads 462 in the chamber 367. The beads are agitated by thedynamic pressure pulses in the chamber and rupture the cells or viruses.In experimental testing, the applicants have found that it is usuallynecessary to use beads to disrupt certain types of cells (particularlyspores) having highly resistant cell walls. Other types of cells, suchas blood cells, are easier to disrupt and may often be disrupted withoutthe use of the beads 462.

[0197] Although the use of an ultrasonic transducer has been describedas a preferred embodiment, it is to be understood that different typesof transducers may be employed in the practice of the present invention.The transducer should be capable of creating pressure pulses or pressurewaves in the chamber 367. In addition, the transducer should be capableof providing high velocity impacts to the liquid in the chamber.Suitable transducers include ultrasonic, piezoelectric,magnetostrictive, or electrostatic transducer. The transducer may alsobe an electromagnetic device having a wound coil, such as a voice coilmotor or a solenoid device. The vibrating frequency of the transducermay be ultrasonic (i.e., above 20 kHz) or below ultrasonic (e.g., in therange of 60 to 20,000 Hz). The advantage to using higher frequencies isthat cell disruption is very rapid and can often be completed in 10 to20 seconds. The disadvantage is that ultrasonic transducers are oftenmore expensive than a simple mechanical vibrator, e.g., a speaker orelectromagnetic coil device. In one alternative embodiment, for example,the solid wall 488 is used in combination with a speaker orelectromagnetic coil device that vibrates at an operating frequency inthe range of 5 to 10 kHz.

[0198] FIGS. 43A-43B illustrate another solid wall 500 for contacting atransducer according to the present invention. As shown in FIG. 43A, oneside of the wall 500 has a central portion 502 and a plurality ofstiffening ribs 504 extending radially from the central portion 502. Thewall also has recesses 506 formed between the ribs 504. As shown in FIG.43B, the other side of the wall 500 has a flat surface 508. FIG. 44shows a partially-cut away isometric view of the container 358 with thewall 500. The wall 500 is preferably positioned so that the side of thewall having the flat surface is internal to the chamber 367 and suchthat the side of the wall having the ribs 504 is external to thechamber. The ribs 504 are advantageous because they increase the naturalfrequency of the wall without causing the wall to be so stiff that itcannot transfer the vibratory movements of the transducer to the chamber367.

[0199]FIG. 45 shows a bottom plan view of the container 358 having thewall 500. The central portion 502 provides the external surface of thewall 500 for contacting a transducer. The interaction of the wall 500with the transducer is analogous to the interaction of the wall 488 withthe transducer previously described with reference to FIG. 41. Inparticular, the wall 500 remains in contact with the tip of thetransducer because the wall 500 has a natural frequency higher than thevibrating frequency of the transducer. Consequently, pressurization isnot required, and cavitation may be achieved. The solid walls 488, 500described with reference to FIGS. 41-45 may be used in the container 358or the walls 488, 500 may be used in a fully integrated cartridge, suchas the cartridge shown in FIG. 1.

[0200] Although the above description contains many specificities, theseshould not be construed as limitations on the scope of the invention,but merely as illustrations of some of the presently preferredembodiments. Many possible variations and modifications to the inventionwill be apparent to one skilled in the art upon consideration of thisdisclosure.

[0201] Therefore, the scope of the invention should be determined by thefollowing claims and their legal equivalents.

What is claimed is:
 1. A device for use with a transducer to separate ananalyte from a fluid sample, the device comprising a cartridge having:a) a sample flow path; b) a lysing chamber in the sample flow path forlysing cells or viruses to release the analyte therefrom, wherein thelysing chamber contains at least one filter for capturing the cells orviruses from the sample as the sample flows through the lysing chamber,the cartridge includes at least one wall defining the lysing chamber,and the wall has an external surface for contacting the transducer tosonicate the lysing chamber; c) a waste chamber in fluid communicationwith the lysing chamber via the sample flow path for receiving theremaining sample fluid after the sample flows through the lysingchamber; d) a third chamber connected to the lysing chamber via ananalyte flow path for receiving the analyte separated from the sample;and e) at least one flow controller for directing the sample into thewaste chamber after the sample flows through the lysing chamber and fordirecting the analyte separated from the sample into the third chamber.2. The device of claim 1, wherein the third chamber comprises a mixingchamber for mixing the analyte with one or more reagents.
 3. The deviceof claim 2, wherein the cartridge further includes a reaction chamber influid communication with the mixing chamber for holding the analyte forchemical reaction or optical detection.
 4. The device of claim 2,wherein the cartridge further includes: i) a reaction chamber in fluidcommunication with the mixing chamber for amplifying the analyte; andii) a capillary electrophoresis area in communication with the reactionchamber.
 5. The device of claim 1, wherein the third chamber comprises areaction chamber for amplifying the analyte and holding the analyte foroptical detection, and wherein the cartridge is in combination with aninstrument having a heater for heating the reaction chamber and havingat least one optical detector for detecting the analyte.
 6. The deviceof claim 1, wherein the third chamber comprises a reaction chamber foramplifying the analyte, and the cartridge further comprises a capillaryelectrophoresis area in communication with the reaction chamber.
 7. Thedevice of claim 1, wherein the wall is dome-shaped and convex withrespect to the transducer.
 8. The device of claim 1, wherein the wallcomprises a sheet or film of polymeric material.
 9. The device of claim8, wherein the wall has a thickness in the range 0.025 to 0.1 mm. 10.The device of claim 1, wherein the wall has stiffening ribs.
 11. Thedevice of claim 10, wherein the ribs extend radially from a centralportion of the wall.
 12. The device of claim 1, further comprising beadsdisposed in the lysing chamber for rupturing the cells or viruses. 13.The device of claim 12, wherein the beads further have a bindingaffinity for the cells or viruses to be disrupted.
 14. The device ofclaim 12, wherein the beads further have a binding affinity for theanalyte.
 15. The device of claim 1, wherein the lysing chamber containsa first set of beads for binding the cells or viruses and a second setof beads for rupturing the cells or viruses.
 16. The device of claim 1,wherein the cartridge includes a first filter in the sample flow pathfor filtering coarse material from the sample and a second filter in thelysing chamber, the second filter having a smaller average pore sizethan the first filter
 17. The device of claim 16, wherein both the firstand second filters are positioned in the lysing chamber, and whereinbeads are disposed between the filters.
 18. The device of claim 17,further comprising a third filter in the lysing chamber, wherein thethird filter is spaced from the second filter, and the third filter hasa smaller average pore size than the second filter.
 19. The device ofclaim 18, wherein the cartridge includes a first set of beads disposedbetween the first and second filters and a second set of beads disposedbetween the second and third filters.
 20. The device of claim 19,wherein the average diameter of the beads in the first set differs fromthe average diameter of the beads in the second set.